1 Background

This report shows the analysis performed for metagenomics sequencing from the gut microbiome of 32 pregnant women. For each pregnant woman, samples were taken at 3 different time points during the pregnancy (i.e. corresponding to trimesters, up until day ~280 when the child is born) to give a total of 96 samples. From the 32 pregnant women, 16 are diabetic (T1D). For some analyses, time points were categorised into trimesters, correspondence being:

Trimester 1 = 0-99 days Trimester 2 = 100-196 days Trimester 3 = 196-280 days

2 Data generation

Samples were shotgun sequenced using the NovaSeq 6000 illumina sequencing machine at the Ramaciotti Centre for Genomics located at the University of New South Wales (UNSW) in Sydney, Australia.

2.1 Processing the sequences: from sequence data to feature table

The data was processed through pipelines developed by the group of Curtis Huttenhower at Harvard Univerisity and Broad Institute. These pipelines belong to the BioBakery.

The raw data was uploaded to the short read archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra/) with accession number PRJNA604850.

  1. KneadData (https://bitbucket.org/biobakery/biobakery/wiki/kneaddata) was used to filter human (“contaminant”) sequences as well as quality controlling the sequences This has to be done for each sample. Example:
  • kneaddata –input 4_S1_R1_001.fastq.gz –input 4_S1_R2_001.fastq.gz -db /home/users/allstaff/schulze.a/bin/Kneaddata/Homo_sapiens –trimmomatic /usr/local/bioinfsoftware/trimmomatic/trimmomatic-0.36 –output ./kneaddata_output -t 12
  1. HUMAnN2 (https://bitbucket.org/biobakery/humann2/wiki/Home) was employed to quantify gene families and pathways; and within HUMANn2, Metaphlan was also used to obtain taxonomic profiles. This process is also performed per sample and read pair1 and read pair2 need to be concatenated and saved in the same file prior to running HUMAn2 (i.e. end-pairing relationships are currently not taken into account during HUMAnN2’s alignment steps. This is due to the fact that HUMAnN2 strictly aligns reads to isolated coding sequences: either at the nucleotide level or through translated search. As such, it will frequently be the case that one read (READ1) will map inside a given coding sequence while its mate-pair (READ2) will not [information obtained from the manual]). Example of running HUMAnN2 with a sample:
  • humann2 -i NGU5366A1.fastq -o ./Output_HUMAnN2 –threads 28
  1. Running this outputs several files, among those is “NGU5366A1_metaphlan_bugs_list.tsv”, which is a list of the bacterial taxa found in that sample at all taxonomic levels (i.e. stratified data) and their relative normalizaed abundances. The script merge_metaphlan_tables.py was used to merge the MetaPhlAn output from several samples into one table taxa (rows) vs samples (columns) with the table enlisting the relative normalized abundances per sample per taxa. Example:
  • merge_metaphlan_tables.py metaphlan_output1.txt metaphlan_output2.txt metaphlan_output3.txt > ./merged_abundance_table_Rel_Abundance.txt
  1. As mentioned above, the abundance table (profile) contains the stratified data. In order to obtain a table that contains the taxa at a specific taxonomic level (e.g. Species), grep was used. Example for species taxonomic level:
  • grep ’s__’ merged_abundance_table_Rel_Abundance.txt | grep -v ’t’ > merged_abundance_table_Rel_Abundance_Sp.tsv # -v (exclude) ’t’ will prevent from selecting those lines that have species and strain (’t__’) classification. We just need species in this case.

Example for genus taxonomic level:

  • grep ’g__’ merged_abundance_table_Rel_Abundance.txt | grep -v ’t’ | grep -v ’s’ > merged_abundance_table_Rel_Abundance_Genus.tsv

Note: For other taxonomic levels, this process was repeated for each taxonomic level.

  1. This table contains the whole taxonomy for each taxa, from “kindom” to “Species” along with per sample abundances. Taxa classified as virus were removed. From this table the taxonomy (“Species_taxonomy.txt”) and the taxa (species) table (“merged_abundance_table_Rel_Abundance_Sp.tsv”) files were constructed. The taxa table is then transformed into a biom file in JSON format and the taxonomic and metadata infomation were added with the software biom. Example:
  • biom convert -i merged_abundance_table_Rel_Abundance_Sp.tsv -o merged_abundance_table_Rel_Abundance_Sp.biom –table-type=“OTU table” –to-json
  • biom add-metadata –sc-separated taxonomy –observation-header OTUID,taxonomy –observation-metadata-fp Species_taxonomy.txt -i merged_abundance_table_Rel_Abundance_Sp.biom -o Pregnancy_NovaSeq_taxonomic_profile_Rel_Species_NV_wTax.biom
  • biom add-metadata -i Pregnancy_NovaSeq_taxonomic_profile_Rel_Species_NV_wTax.biom -o Pregnancy_NovaSeq_taxonomic_profile_Rel_Species_NV_wTaxMet.biom –sample-metadata-fp ./metadata.csv

This process was repeated at for each taxonomic level.

The resulting taxa tables (one for each taxonomic level) with taxonomies and metadata were imported into R to process with the Phyloseq (https://github.com/joey711/phyloseq) and other packages. The data were first de-identified (i.e. data relating to the identification of the donor was removed) and R object were saved. Those R objects were used as inputs in the analysis performed in this document.

3 Bar plots taxonomy

4 Alpha diversity

4.1 Alpha diversity (T1D vs. non-T1D continuous time [Days])


Call:
geeglm(formula = Observed ~ t1dfactor * days_c + age_c + nullip + 
    bmi_c + HLA, data = DivCal_R_df, id = motherid, corstr = "exchangeable")

 Coefficients:
                     Estimate   Std.err     Wald Pr(>|W|)    
(Intercept)         102.56782   2.40649 1816.586  < 2e-16 ***
t1dfactorT1D         -0.12034   2.16713    0.003  0.95572    
days_c                0.01784   0.02019    0.781  0.37689    
age_c                -0.22778   0.34311    0.441  0.50678    
nullipYes            -3.17432   2.54254    1.559  0.21185    
bmi_c                -0.44837   0.27895    2.584  0.10798    
HLADRXX              -9.12498   2.95011    9.567  0.00198 ** 
HLAGroup3o4          -4.98593   2.80853    3.152  0.07585 .  
t1dfactorT1D:days_c  -0.04773   0.03375    2.000  0.15731    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Estimated Scale Parameters:
            Estimate Std.err
(Intercept)    104.2   12.54

Correlation: Structure = exchangeable  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha   0.1932   0.127
Number of clusters:   83   Maximum cluster size: 3 

4.2 Alpha diversity (T1D vs. non-T1D categorical time [Trimester])


Call:
geeglm(formula = Observed ~ t1dfactor * Tri + age_c + nullip + 
    bmi_c + HLA, data = DivCal_R_df, id = motherid, corstr = "exchangeable")

 Coefficients:
                   Estimate Std.err   Wald Pr(>|W|)    
(Intercept)         103.100   3.355 944.63   <2e-16 ***
t1dfactorT1D          2.795   4.164   0.45   0.5020    
TriT2                -1.873   2.928   0.41   0.5224    
TriT3                 2.587   3.555   0.53   0.4668    
age_c                -0.236   0.342   0.48   0.4892    
nullipYes            -2.984   2.572   1.35   0.2459    
bmi_c                -0.451   0.276   2.68   0.1017    
HLADRXX              -9.841   3.043  10.46   0.0012 ** 
HLAGroup3o4          -5.701   2.964   3.70   0.0545 .  
t1dfactorT1D:TriT2   -1.973   5.090   0.15   0.6982    
t1dfactorT1D:TriT3   -6.788   5.714   1.41   0.2349    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Estimated Scale Parameters:
            Estimate Std.err
(Intercept)      104    12.4

Correlation: Structure = exchangeable  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha     0.26   0.137
Number of clusters:   83   Maximum cluster size: 3 

5 Species taxonomic level

5.1 Microbial community composition analysis at Species level (Beta diversity analysi)

Hypothesis

Hypothesis: the gut microbiome taxonomic composition (i.e. Beta diversity) during pregnancy differs between women with and without T1D. In order to test if this hypothesis holds true, a measurement of the distance between each pair of samples is calculated (i.e. Bray-Curtis) and a repeated measure aware permutational analysis of variance (i.e. RMA-PERMANOVA) test is applied. A P-value <0.05 is considered to be significant, meaning that our hypothesis cannot be rejected. Borderline P-values are also considered positive.

Problems with the available R function for Beta diversity analysis

The current available function for performing hypothesis testing of differences in the microbiome composition between groups of samples is called Adonis (i.e. which perform a PERMANOVA test) and is part of the Rpackage vegan (Oksanen, J. et al). The main problem with this function is that if the metadata of interest does not vary with time (e.g. disease status, sex, etc.), adonis does not calculate the corresponding P value correctly, as it permutes levels within a subject. This does not make sense for something like disease status or sex as permuting within-subject will produce the exact same distribution each time you permute. This a known drawback of the adonis function for repeated measures.

In order to get the correct P-value for a time-invariant metadata, the permutation procedure has to be altered such that it permutes the subjects rather than levels within subjects, which apply to our current pregnancy dataset.

Here I’m running a script written by Jason Lloyd-Price from Curtis Huttenhower lab in Harvard. This script is being used instead of the regular Adonis (PERMANOVA test) from the R package Vegan because as stated above, our metadata of interest (i.e. T1D status) does not vary with time, we have a mixture of data which changes within and between an individual and we also have unequal group sizes (i.e. we do not always have exactly 3 samples per woman). For those three reasons, it was recommended to use his script to perform the RMA-PERMANOVA analysis.

PARAMETERS:

permute_within: This data frame has samples on rows and metadata on columns. This should only contain metadata that varies within a block (i.e. it’s a single-column data frame with only time/Days).Since, the other metadata within the block should be the same between repeated measurements and this will not hold when we introduce other factor i.e. sequencing run, BMI, parity, gestational age (i.e. Days or trimester) and conception age , those five factors should be placed here

blocks: This should just be a vector giving the group of each sample (i.e. the motherid vector; motherid is strictly accounting for personID but not for pregnancy per se).

block_data: This data frame contains per-block metadata, with one row per block (motherid). It should only contain metadata pertaining to the blocks (i.e. T1Dstatus). motherid is not numeric, ensure that the row names match the factor names in the motherid vector (blocks).

metadata_order: This is needed if you want to specify a particular order that the model should be fit in. Metadata earlier in the list will be fit and residualized first, so these should be features we are NOT interested in and want to control for.

Results from PERMANOVA test with repeat measure-aware permutations - Controlling for Days/Trimester, sequencing run, conception age, BMI, parity and HLA type

Here the blocking factor is taking into account each mother who might have given samples from different trimesters or two different pregnancies (i.e. motherid is the name of the factor). Therefore, the factor “motherid” takes into account two different pregnancies from the same mother as one SubjectID to adjust for repeated measurements

The interaction between T1D status and time was also included in order to test if the differences between T1D and non-T1D women in the same or changes throguhout pregnancy.

5.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun                3      1.59   0.529    2.93 0.076  0.002 ** 
Days                  1      0.13   0.130    0.72 0.006  0.177    
T1D_Time_Interaction  1      0.70   0.702    3.89 0.034  0.001 ***
Age                   1      0.61   0.609    3.37 0.029  0.980    
Parity                1      0.60   0.601    3.33 0.029  0.231    
BMI                   1      0.55   0.546    3.02 0.026  0.882    
HLA                   2      1.36   0.682    3.77 0.065  0.080 .  
T1Dstatus             1      0.23   0.229    1.27 0.011  0.993    
Residuals            84     15.18   0.181         0.725  0.319    
Total                95     20.95                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.001

Due to the interaction between T1D and time having a significant P-value, differences in beta diversity between T1D and non-T1D was assessed by trimester using a normal PERMANOVA with the adonis function.

5.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3      0.57   0.191   0.800 0.111   0.88
Nulliparous     1      0.34   0.337   1.414 0.065   0.11
Age_LMP         1      0.24   0.238   1.001 0.046   0.47
BMI_conception  1      0.26   0.263   1.104 0.051   0.35
HLA.6DRML       2      0.36   0.178   0.747 0.069   0.89
T1Dstatus       1      0.28   0.283   1.187 0.055   0.25
Residuals      13      3.10   0.238         0.602       
Total          22      5.14                 1.000       
[1] 0.253

Beta diversity Plot

5.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3      0.71   0.237    1.12 0.103  0.229  
Nulliparous     1      0.25   0.251    1.19 0.036  0.225  
Age_LMP         1      0.25   0.253    1.20 0.037  0.235  
BMI_conception  1      0.24   0.241    1.14 0.035  0.291  
HLA.6DRML       2      0.51   0.255    1.21 0.074  0.150  
T1Dstatus       1      0.31   0.312    1.48 0.045  0.067 .
Residuals      22      4.65   0.211         0.671         
Total          31      6.92                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.067

Beta diversity Plot

5.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
SeqRun          3      0.71   0.237    1.16 0.103  0.187    
Nulliparous     1      0.21   0.210    1.02 0.030  0.428    
Age_LMP         1      0.29   0.291    1.42 0.042  0.081 .  
BMI_conception  1      0.28   0.279    1.36 0.040  0.088 .  
HLA.6DRML       2      0.47   0.234    1.14 0.068  0.228    
T1Dstatus       1      0.44   0.442    2.16 0.064  0.001 ***
Residuals      22      4.50   0.205         0.652           
Total          31      6.90                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.001

Beta diversity Plot

5.1.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.14   0.572    4.05 0.112  0.265  
seqRun     3      1.74   0.580    4.11 0.171  0.319  
Age        1      0.56   0.564    3.99 0.055  0.857  
Parity     1      0.67   0.666    4.71 0.065  0.033 *
BMI        1      0.58   0.575    4.07 0.056  0.755  
Days       1      0.13   0.133    0.94 0.013  0.068 .
Residuals 38      5.37   0.141         0.527  0.163  
Total     47     10.19                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

5.1.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.14   0.572    4.01 0.112  0.263  
seqRun     3      1.74   0.580    4.07 0.171  0.291  
Age        1      0.56   0.564    3.95 0.055  0.855  
Parity     1      0.67   0.666    4.66 0.065  0.036 *
BMI        1      0.58   0.575    4.03 0.056  0.737  
Tri        2      0.22   0.110    0.77 0.022  0.183  
Residuals 37      5.28   0.143         0.518  0.150  
Total     47     10.19                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

5.1.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      1.35   0.675    5.00 0.135  0.122   
seqRun     3      1.55   0.517    3.82 0.155  0.816   
Age        1      1.17   1.168    8.65 0.117  0.009 **
Parity     1      0.37   0.375    2.78 0.037  0.983   
BMI        1      0.30   0.297    2.20 0.030  0.823   
Days       1      0.16   0.155    1.15 0.015  0.035 * 
Residuals 38      5.13   0.135         0.512  0.040 * 
Total     47     10.03                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

5.1.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      1.35   0.675    4.88 0.135  0.114   
seqRun     3      1.55   0.517    3.74 0.155  0.838   
Age        1      1.17   1.168    8.45 0.117  0.006 **
Parity     1      0.37   0.375    2.71 0.037  0.989   
BMI        1      0.30   0.297    2.15 0.030  0.835   
Tri        2      0.17   0.087    0.63 0.017  0.602   
Residuals 37      5.11   0.138         0.510  0.100 . 
Total     47     10.03                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

5.1.9 Other factors

5.1.9.1 Age at conception

5.1.9.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.38 0.059  0.225  
T1Dstatus             1      0.85   0.848    4.66 0.040  0.037 *
seqRun                3      1.66   0.554    3.05 0.079  0.203  
Tri                   2      0.24   0.121    0.67 0.012  0.465  
Age                   1      0.61   0.610    3.35 0.029  0.306  
Parity                1      0.54   0.544    2.99 0.026  0.826  
BMI                   1      0.57   0.566    3.11 0.027  0.578  
Age_Time_Interaction  1      0.14   0.144    0.79 0.007  0.105  
Residuals            83     15.10   0.182         0.721  0.036 *
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.37 0.059  0.255  
T1Dstatus             1      0.85   0.848    4.64 0.040  0.038 *
seqRun                3      1.66   0.554    3.03 0.079  0.190  
Tri                   2      0.24   0.121    0.66 0.012  0.465  
Age                   1      0.61   0.610    3.34 0.029  0.290  
Parity                1      0.54   0.544    2.98 0.026  0.827  
BMI                   1      0.57   0.566    3.10 0.027  0.588  
Age_Time_Interaction  1      0.08   0.082    0.45 0.004  0.684  
Residuals            83     15.16   0.183         0.724  0.050 *
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.37 0.059  0.218  
T1Dstatus             1      0.85   0.848    4.65 0.040  0.026 *
seqRun                3      1.66   0.554    3.04 0.079  0.201  
Tri                   2      0.24   0.121    0.66 0.012  0.497  
Age                   1      0.61   0.610    3.34 0.029  0.287  
Parity                1      0.54   0.544    2.98 0.026  0.817  
BMI                   1      0.57   0.566    3.10 0.027  0.615  
Age_Time_Interaction  1      0.10   0.099    0.54 0.005  0.256  
Residuals            83     15.15   0.182         0.723  0.037 *
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.1.4 Age at conception (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.23   0.616    3.39 0.059  0.221  
T1Dstatus  1      0.85   0.848    4.67 0.040  0.028 *
seqRun     3      1.66   0.554    3.05 0.079  0.215  
Tri        2      0.24   0.121    0.67 0.012  0.456  
Parity     1      0.53   0.534    2.94 0.026  0.831  
BMI        1      0.59   0.592    3.26 0.028  0.423  
Age        1      0.59   0.593    3.27 0.028  0.503  
Residuals 84     15.25   0.181         0.728  0.045 *
Total     95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

5.1.9.2 Body max index (BMI)

5.1.9.2.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.37 0.059  0.214  
T1Dstatus             1      0.85   0.848    4.64 0.040  0.038 *
seqRun                3      1.66   0.554    3.03 0.079  0.205  
Tri                   2      0.24   0.121    0.66 0.012  0.484  
Age                   1      0.61   0.610    3.34 0.029  0.291  
Parity                1      0.54   0.544    2.98 0.026  0.832  
BMI                   1      0.57   0.566    3.10 0.027  0.596  
BMI_Time_Interaction  1      0.09   0.092    0.50 0.004  0.684  
Residuals            83     15.15   0.183         0.723  0.059 .
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.2.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.36 0.059  0.219  
T1Dstatus             1      0.85   0.848    4.63 0.040  0.026 *
seqRun                3      1.66   0.554    3.03 0.079  0.199  
Tri                   2      0.24   0.121    0.66 0.012  0.508  
Age                   1      0.61   0.610    3.33 0.029  0.316  
Parity                1      0.54   0.544    2.97 0.026  0.826  
BMI                   1      0.57   0.566    3.09 0.027  0.566  
BMI_Time_Interaction  1      0.05   0.050    0.27 0.002  0.982  
Residuals            83     15.20   0.183         0.725  0.056 .
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.2.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.37 0.059  0.230  
T1Dstatus             1      0.85   0.848    4.64 0.040  0.025 *
seqRun                3      1.66   0.554    3.03 0.079  0.203  
Tri                   2      0.24   0.121    0.66 0.012  0.458  
Age                   1      0.61   0.610    3.34 0.029  0.308  
Parity                1      0.54   0.544    2.98 0.026  0.816  
BMI                   1      0.57   0.566    3.10 0.027  0.573  
BMI_Time_Interaction  1      0.09   0.091    0.50 0.004  0.113  
Residuals            83     15.15   0.183         0.723  0.033 *
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.2.4 BMI (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.23   0.616    3.39 0.059  0.217  
T1Dstatus  1      0.85   0.848    4.67 0.040  0.038 *
seqRun     3      1.66   0.554    3.05 0.079  0.200  
Tri        2      0.24   0.121    0.67 0.012  0.473  
Age        1      0.61   0.610    3.36 0.029  0.316  
Parity     1      0.54   0.544    3.00 0.026  0.835  
BMI        1      0.57   0.566    3.12 0.027  0.583  
Residuals 84     15.25   0.181         0.728  0.033 *
Total     95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

5.1.9.3 HLA type

5.1.9.3.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.39 0.059  0.231  
T1Dstatus             1      0.85   0.848    4.66 0.040  0.044 *
Days                  1      0.13   0.131    0.72 0.006  0.220  
seqRun                3      1.66   0.552    3.04 0.079  0.189  
Age                   1      0.60   0.601    3.30 0.029  0.371  
Parity                1      0.55   0.545    3.00 0.026  0.828  
BMI                   1      0.56   0.561    3.09 0.027  0.618  
HLA_Time_Interaction  1      0.10   0.104    0.57 0.005  1.000  
Residuals            84     15.27   0.182         0.729  0.594  
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.3.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.39 0.059   0.24  
T1Dstatus             1      0.85   0.848    4.66 0.040   0.04 *
Days                  1      0.13   0.131    0.72 0.006   0.19  
seqRun                3      1.66   0.552    3.04 0.079   0.19  
Age                   1      0.60   0.601    3.30 0.029   0.41  
Parity                1      0.55   0.545    3.00 0.026   0.81  
BMI                   1      0.56   0.561    3.09 0.027   0.60  
HLA_Time_Interaction  1      0.10   0.099    0.55 0.005   1.00  
Residuals            84     15.28   0.182         0.729   0.32  
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.3.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.39 0.059  0.223  
T1Dstatus             1      0.85   0.848    4.67 0.040  0.028 *
Days                  1      0.13   0.131    0.72 0.006  0.195  
seqRun                3      1.66   0.552    3.04 0.079  0.222  
Age                   1      0.60   0.601    3.31 0.029  0.369  
Parity                1      0.55   0.545    3.00 0.026  0.818  
BMI                   1      0.56   0.561    3.09 0.027  0.614  
HLA_Time_Interaction  1      0.13   0.129    0.71 0.006  1.000  
Residuals            84     15.25   0.182         0.728  0.277  
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.3.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1      0.14   0.139    0.77 0.007  0.149  
seqRun     3      1.58   0.526    2.91 0.075  0.631  
Age        1      0.59   0.585    3.23 0.028  0.958  
Parity     1      0.61   0.607    3.35 0.029  0.146  
BMI        1      0.58   0.580    3.21 0.028  0.731  
T1Dstatus  1      0.69   0.688    3.80 0.033  0.168  
HLA        2      1.40   0.699    3.86 0.067  0.082 .
Residuals 85     15.38   0.181         0.734  0.043 *
Total     95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

5.1.9.4 Parity

5.1.9.4.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      1.23   0.616    3.39 0.059  0.233  
T1Dstatus                1      0.85   0.848    4.67 0.040  0.044 *
Days                     1      0.13   0.131    0.72 0.006  0.197  
seqRun                   3      1.66   0.552    3.04 0.079  0.224  
Age                      1      0.60   0.601    3.31 0.029  0.365  
Parity                   1      0.55   0.545    3.00 0.026  0.828  
BMI                      1      0.56   0.561    3.09 0.027  0.621  
Parity_Time_Interaction  1      0.12   0.116    0.64 0.006  0.155  
Residuals               84     15.26   0.182         0.728  0.038 *
Total                   95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.4.2 Parity (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.23   0.616    3.40 0.059  0.254  
T1Dstatus  1      0.85   0.848    4.69 0.040  0.044 *
Days       1      0.13   0.131    0.72 0.006  0.213  
seqRun     3      1.66   0.552    3.05 0.079  0.193  
BMI        1      0.72   0.717    3.97 0.034  0.452  
Age        1      0.59   0.589    3.26 0.028  0.501  
Parity     1      0.40   0.401    2.22 0.019  0.878  
Residuals 85     15.38   0.181         0.734  0.042 *
Total     95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

5.1.9.5 Mode of delivery

5.1.9.5.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.57 0.059  0.259  
T1Dstatus             1      0.85   0.848    4.92 0.040  0.026 *
MOD                   2      1.08   0.539    3.12 0.051  0.469  
Days                  1      0.13   0.130    0.76 0.006  0.194  
seqRun                3      1.58   0.527    3.06 0.075  0.484  
Age                   1      0.68   0.681    3.95 0.032  0.076 .
Parity                1      0.53   0.527    3.06 0.025  0.808  
BMI                   1      0.62   0.617    3.58 0.029  0.341  
MOD_Time_Interaction  1      0.12   0.117    0.68 0.006  1.000  
Residuals            82     14.14   0.172         0.675  0.435  
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.5.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.56 0.059  0.200  
T1Dstatus             1      0.85   0.848    4.90 0.040  0.031 *
MOD                   2      1.08   0.539    3.11 0.051  0.487  
Days                  1      0.13   0.130    0.75 0.006  0.193  
seqRun                3      1.58   0.527    3.05 0.075  0.477  
Age                   1      0.68   0.681    3.93 0.032  0.088 .
Parity                1      0.53   0.527    3.05 0.025  0.789  
BMI                   1      0.62   0.617    3.56 0.029  0.363  
MOD_Time_Interaction  1      0.07   0.069    0.40 0.003  1.000  
Residuals            82     14.19   0.173         0.677  0.212  
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.5.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.23   0.616    3.56 0.059  0.222  
T1Dstatus             1      0.85   0.848    4.90 0.040  0.035 *
MOD                   2      1.08   0.539    3.12 0.051  0.460  
Days                  1      0.13   0.130    0.75 0.006  0.162  
seqRun                3      1.58   0.527    3.05 0.075  0.492  
Age                   1      0.68   0.681    3.94 0.032  0.081 .
Parity                1      0.53   0.527    3.05 0.025  0.793  
BMI                   1      0.62   0.617    3.57 0.029  0.339  
MOD_Time_Interaction  1      0.08   0.081    0.47 0.004  1.000  
Residuals            82     14.17   0.173         0.677  0.328  
Total                95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.5.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1      0.14   0.139    0.81 0.007  0.168  
seqRun     3      1.58   0.526    3.06 0.075  0.665  
Age        1      0.59   0.585    3.41 0.028  0.948  
Parity     1      0.61   0.607    3.53 0.029  0.152  
BMI        1      0.58   0.580    3.38 0.028  0.739  
HLA        2      1.21   0.603    3.51 0.058  0.257  
T1Dstatus  1      0.88   0.880    5.12 0.042  0.024 *
MOD        2      1.12   0.560    3.26 0.053  0.402  
Residuals 83     14.26   0.172         0.681  0.065 .
Total     95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

5.1.9.6 Carbohydrate intake

5.1.9.6.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.23   0.616    3.43 0.059  0.223  
T1Dstatus              1      0.85   0.848    4.72 0.040  0.035 *
Carbs                  1      0.45   0.455    2.53 0.022  0.722  
seqRun                 3      1.65   0.550    3.06 0.079  0.249  
Tri                    2      0.24   0.118    0.66 0.011  0.458  
Age                    1      0.55   0.553    3.08 0.026  0.702  
Parity                 1      0.54   0.538    3.00 0.026  0.775  
BMI                    1      0.60   0.605    3.37 0.029  0.380  
Carb_Time_Interaction  1      0.10   0.104    0.58 0.005  0.966  
Residuals             82     14.73   0.180         0.703  0.155  
Total                 95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.6.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.23   0.616    3.41 0.059  0.246  
T1Dstatus              1      0.85   0.848    4.70 0.040  0.048 *
Carbs                  1      0.45   0.455    2.52 0.022  0.684  
seqRun                 3      1.65   0.550    3.05 0.079  0.257  
Tri                    2      0.24   0.118    0.66 0.011  0.457  
Age                    1      0.55   0.553    3.07 0.026  0.695  
Parity                 1      0.54   0.538    2.99 0.026  0.797  
BMI                    1      0.60   0.605    3.35 0.029  0.402  
Carb_Time_Interaction  1      0.04   0.043    0.24 0.002  1.000  
Residuals             82     14.79   0.180         0.706  0.260  
Total                 95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.6.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.23   0.616    3.42 0.059  0.271  
T1Dstatus              1      0.85   0.848    4.71 0.040  0.035 *
Carbs                  1      0.45   0.455    2.53 0.022  0.723  
seqRun                 3      1.65   0.550    3.06 0.079  0.274  
Tri                    2      0.24   0.118    0.66 0.011  0.477  
Age                    1      0.55   0.553    3.07 0.026  0.688  
Parity                 1      0.54   0.538    2.99 0.026  0.818  
BMI                    1      0.60   0.605    3.36 0.029  0.389  
Carb_Time_Interaction  1      0.07   0.070    0.39 0.003  0.995  
Residuals             82     14.76   0.180         0.705  0.186  
Total                 95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.6.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3      1.59   0.529    2.96 0.076  0.001 ***
Tri        2      0.26   0.130    0.73 0.012  0.475    
Age        1      0.59   0.594    3.33 0.028  0.622    
Parity     1      0.61   0.609    3.41 0.029  0.200    
BMI        1      0.58   0.578    3.23 0.028  0.845    
HLA        2      1.19   0.594    3.33 0.057  0.241    
T1Dstatus  1      0.89   0.888    4.97 0.042  0.022 *  
Carbs      1      0.41   0.414    2.31 0.020  0.795    
Residuals 83     14.83   0.179         0.708  0.098 .  
Total     95     20.95                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

5.1.9.7 Fibre intake

5.1.9.7.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      1.23   0.616    3.40 0.059  0.222  
T1Dstatus               1      0.85   0.848    4.69 0.040  0.034 *
Fiber                   1      0.35   0.352    1.95 0.017  0.940  
seqRun                  3      1.62   0.541    2.99 0.077  0.345  
Tri                     2      0.24   0.122    0.67 0.012  0.413  
Age                     1      0.57   0.574    3.18 0.027  0.589  
Parity                  1      0.54   0.544    3.00 0.026  0.757  
BMI                     1      0.60   0.603    3.33 0.029  0.415  
Fiber_Time_Interaction  1      0.10   0.097    0.53 0.005  0.929  
Residuals              82     14.83   0.181         0.708  0.198  
Total                  95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.7.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      1.23   0.616    3.39 0.059  0.249  
T1Dstatus               1      0.85   0.848    4.67 0.040  0.037 *
Fiber                   1      0.35   0.352    1.94 0.017  0.937  
seqRun                  3      1.62   0.541    2.98 0.077  0.348  
Tri                     2      0.24   0.122    0.67 0.012  0.460  
Age                     1      0.57   0.574    3.16 0.027  0.569  
Parity                  1      0.54   0.544    2.99 0.026  0.773  
BMI                     1      0.60   0.603    3.32 0.029  0.402  
Fiber_Time_Interaction  1      0.04   0.043    0.24 0.002  1.000  
Residuals              82     14.89   0.182         0.711  0.332  
Total                  95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.7.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      1.23   0.616    3.40 0.059  0.230  
T1Dstatus               1      0.85   0.848    4.68 0.040  0.023 *
Fiber                   1      0.35   0.352    1.94 0.017  0.925  
seqRun                  3      1.62   0.541    2.98 0.077  0.323  
Tri                     2      0.24   0.122    0.67 0.012  0.451  
Age                     1      0.57   0.574    3.17 0.027  0.534  
Parity                  1      0.54   0.544    3.00 0.026  0.764  
BMI                     1      0.60   0.603    3.33 0.029  0.411  
Fiber_Time_Interaction  1      0.07   0.073    0.40 0.003  0.992  
Residuals              82     14.86   0.181         0.709  0.239  
Total                  95     20.95                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.7.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3      1.59   0.529    2.94 0.076  0.001 ***
Tri        2      0.26   0.130    0.72 0.012  0.450    
Age        1      0.59   0.594    3.30 0.028  0.643    
Parity     1      0.61   0.609    3.38 0.029  0.203    
BMI        1      0.58   0.578    3.21 0.028  0.813    
HLA        2      1.19   0.594    3.30 0.057  0.259    
T1Dstatus  1      0.89   0.888    4.93 0.042  0.026 *  
Fiber      1      0.31   0.314    1.75 0.015  0.954    
Residuals 83     14.93   0.180         0.713  0.201    
Total     95     20.95                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

5.1.9.8 1,5-AG (glucose control measurement)

5.1.9.8.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.33   0.664    3.86 0.067  0.120  
T1Dstatus             1      0.87   0.868    5.05 0.044  0.029 *
Days                  1      0.12   0.125    0.73 0.006  0.387  
seqRun                3      1.62   0.539    3.13 0.081  0.306  
Age                   1      0.63   0.630    3.66 0.032  0.225  
Parity                1      0.55   0.550    3.20 0.028  0.767  
BMI                   1      0.50   0.499    2.90 0.025  0.750  
AG15                  1      0.59   0.592    3.44 0.030  0.017 *
AG15_T1D_Interaction  1      0.38   0.379    2.20 0.019  0.887  
Residuals            77     13.25   0.172         0.668  0.018 *
Total                89     19.83                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.8.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.16   0.581    4.33 0.128  0.197  
Days       1      0.24   0.239    1.78 0.026  0.020 *
seqRun     3      1.56   0.521    3.89 0.173  0.778  
Age        1      0.45   0.454    3.38 0.050  0.930  
Parity     1      0.69   0.694    5.17 0.077  0.016 *
BMI        1      0.56   0.555    4.14 0.061  0.708  
AG15       1      0.23   0.230    1.71 0.025  0.948  
Residuals 31      4.16   0.134         0.459  0.438  
Total     41      9.05                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
5.1.9.8.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      1.35   0.675    5.34 0.135  0.129   
Days       1      0.15   0.153    1.21 0.015  0.033 * 
seqRun     3      1.56   0.519    4.11 0.155  0.791   
Age        1      1.16   1.164    9.22 0.116  0.008 **
Parity     1      0.38   0.380    3.01 0.038  0.979   
BMI        1      0.29   0.290    2.29 0.029  0.856   
AG15       1      0.46   0.457    3.62 0.046  0.858   
Residuals 37      4.67   0.126         0.466  0.104   
Total     47     10.03                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

5.2 Differential abundance analysis Species taxonomic level

Differential abundance analysis with limma using voom pipeline with structural zeros - Gordon

Improved analysis using TMM normalization and voom with structural zeros.

A linear model is fit to the data and differential abundance is assessed using empirical bayes. The false discovery rate (FDR) for this analysis is set at 5%. For a OTU to be classified as differentially abundant (DA), its change in abundance between the groups (T1D vs nonT1D) must be significant. In the results tables to follow, the genes that are DE are those that have an adjusted p-value less than the FDR. Note that adjusted p-value is used opposed to the initial p-value as it has been adjusted for multiple testing. Therefore any adjusted p-value less than 0.05 is deemed statistically significant, identifying the associated gene as DA.

Those genes that are DA are then determined to be more- or less abundant depending on the direction of their log-fold change. Those OTUs with a positive log-fold change are more abundant, while those OTUs with a negative log-fold change are less abundant.

Controlling for multiple measurements, sequencing run, conception age, BMI, parity and HLA type

       nonT1D_vs_T1D  T1  T2  T3 T1_vs_T2 T2_vs_T3 T1_vs_T3 T1DT1vsT2 T1DT2vsT3 T1DT1vsT3
Down               9   2   1   9        0        0        0         0         0         0
NotSig           288 295 297 288      298      298      298       298       298       298
Up                 1   1   0   1        0        0        0         0         0         0
       noT1DT1vsT2 noT1DT2vsT3 noT1DT1vsT3
Down             0           0           0
NotSig         298         298         298
Up               0           0           0

Differentially abundant species were found between T1D and non-T1D women across pregnancy and within each trimester. No differentially abundant species were detected between trimesters in samples form T1D and non-T1D women together or separatelly.

Results for contrasts with significant differentially abundant species are shown below

5.2.1 Across all trimesters (T1D vs non-T1D)

            Classification  LogFC    P.Val adj.P.Val nonT1D:mean% Prev% T1D:mean%
5    Bacteroides_uniformis -1.373 4.11e-03   0.08745        5.240 100.0     7.768
8         Escherichia_coli -1.046 1.18e-05   0.00176        0.109  87.5     0.869
2    Bacteroides_eggerthii -1.025 6.71e-04   0.03333        0.680 100.0     4.296
6        Alistipes_sp_AP11 -1.007 1.52e-04   0.00904        0.331  41.7     1.551
1       Bacteroides_clarus -0.898 4.87e-05   0.00484        0.011  37.5     0.545
7        Roseburia_hominis -0.784 3.28e-03   0.07975        0.338  93.8     0.775
9 Escherichia_unclassified -0.711 1.01e-03   0.04171        0.027  77.1     0.278
3 Bacteroides_intestinalis -0.660 3.48e-03   0.07975        0.600  62.5     0.228
4 Bacteroides_massiliensis  0.945 1.44e-03   0.04281        2.659 100.0     1.575
  T1D:Prev%
5     100.0
8      89.6
2     100.0
6      50.0
1      60.4
7      93.8
9      79.2
3      60.4
4     100.0

First part of the code used to plot Figure 3 of the article. This and other coded parts in the differential abundance analysis have the specific figures and ordering (i.e. as specified by the letters (Let variable)) of the composed figure used for the manuscript. Note that, as per described in the article, only taxa with prevalence > 50% in either group in the comparison, are considered.

5.2.2 Only Trimester 1 (nonT1D vs T1D)

            Classification  LogFC    P.Val adj.P.Val nonT1D:mean% Prev% T1D:mean%
5         Escherichia_coli -1.362 3.06e-05   0.00912        0.065  72.7     1.374
4        Alistipes_sp_AP11 -1.194 8.40e-04   0.06256        0.145  36.4     1.234
3   Bacteroides_salyersiae -1.044 1.27e-03   0.07302        0.182  18.2     0.611
1       Bacteroides_clarus -0.956 1.47e-03   0.07302        0.029  36.4     0.832
2 Bacteroides_massiliensis  1.535 1.05e-04   0.01557        2.031 100.0     0.282
  T1D:Prev%
5      83.3
4      50.0
3      50.0
1      66.7
2     100.0
[1] 14

5.2.3 Only Trimester 2 (nonT1D vs T1D)

          Classification LogFC    P.Val adj.P.Val mean% Prev%
1 Bacteroides_salyersiae -1.04 0.000134    0.0399 0.087  25.0
2 Bacteroides_salyersiae -1.04 0.000134    0.0399 0.945  37.5

After filtering low prevalent taxa, no species was significantly different between T1D and non-T1D women in this comparison.

5.2.4 Only Trimester 3 (nonT1D vs T1D)

                 Classification  LogFC    P.Val adj.P.Val nonT1D:mean% Prev% T1D:mean%
8         Bacteroides_uniformis -2.071 2.90e-04   0.01150        3.033 100.0     8.692
4         Bacteroides_eggerthii -1.339 1.63e-04   0.01150        0.300 100.0     4.166
2            Bacteroides_caccae -1.323 2.84e-04   0.01150        0.639 100.0     1.905
7        Bacteroides_salyersiae -1.316 3.79e-06   0.00113        0.178  43.8     1.084
10            Roseburia_hominis -1.282 5.65e-05   0.00715        0.244 100.0     0.837
9    Parabacteroides_distasonis -1.206 2.81e-04   0.01150        0.283 100.0     2.068
12    Sutterella_wadsworthensis -1.085 3.89e-03   0.08287        1.050  93.8     1.520
13             Escherichia_coli -1.024 3.09e-04   0.01150        0.163  93.8     0.760
3            Bacteroides_clarus -0.912 5.76e-04   0.01907        0.009  31.2     0.303
6      Bacteroides_intestinalis -0.796 3.17e-03   0.07882        0.238  81.2     0.254
5            Bacteroides_faecis -0.779 4.41e-03   0.08760        0.134  93.8     0.948
14     Escherichia_unclassified -0.750 3.82e-03   0.08287        0.032  81.2     0.232
11          Ruminococcus_bromii  0.976 4.96e-03   0.09241        1.855  93.8     0.305
1  Bifidobacterium_adolescentis  1.056 8.21e-04   0.02447        2.325  81.2     0.083
   T1D:Prev%
8      100.0
4      100.0
2      100.0
7       50.0
10      93.8
9      100.0
12     100.0
13     100.0
3       50.0
6       81.2
5       81.2
14      68.8
11     100.0
1       81.2

5.2.5 T1 vs T2 (All data)

[1] "No DA taxa found"

Nothing left after filtering by prevalence and LogFC

5.2.6 T2 vs T3 (All data)

[1] "No DA taxa"

Nothing left after filtering by prevalence and LogFC

5.2.7 T1 vs T3 (All data)

[1] "No DA taxa found"

5.2.8 T1 vs T2 (in women with T1D)

[1] "No DA taxa found"

5.2.9 T2 vs T3 (in women with T1D)

[1] "No DA taxa found"

5.2.10 T1 vs T3 (in women with T1D)

[1] "No DA taxa found"

5.2.11 T1 vs T2 (in women without T1D)

[1] "No DA taxa found"

5.2.12 T2 vs T3 (in women without T1D)

[1] "No DA taxa found"

5.2.13 T1 vs T3 (in women without T1D)

[1] "No DA taxa found"

6 Strain taxonomic level

6.1 Microbial community composition analysis at strain level (Beta diversity analysis)

6.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
seqRun                3      1.52   0.506    2.64 0.069  0.174   
Days                  1      0.15   0.150    0.78 0.007  0.102   
T1D_Time_Interaction  1      0.80   0.800    4.18 0.036  0.006 **
Age                   1      0.64   0.637    3.33 0.029  0.986   
Parity                1      0.61   0.607    3.17 0.027  0.118   
BMI                   1      0.56   0.556    2.90 0.025  0.797   
HLA                   2      1.51   0.753    3.93 0.068  0.044 * 
T1Dstatus             1      0.26   0.265    1.38 0.012  0.989   
Residuals            84     16.10   0.192         0.727  0.236   
Total                95     22.14                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.006

6.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3      0.56   0.187   0.723 0.102   0.95
Nulliparous     1      0.33   0.334   1.289 0.060   0.18
Age_LMP         1      0.25   0.253   0.978 0.046   0.49
BMI_conception  1      0.29   0.285   1.101 0.052   0.36
HLA.6DRML       2      0.40   0.200   0.774 0.072   0.84
T1Dstatus       1      0.33   0.327   1.265 0.059   0.20
Residuals      13      3.37   0.259         0.609       
Total          22      5.53                 1.000       
[1] 0.195

Beta diversity Plot

6.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3      0.71   0.236    1.07 0.097  0.341  
Nulliparous     1      0.25   0.250    1.13 0.034  0.289  
Age_LMP         1      0.26   0.265    1.20 0.036  0.213  
BMI_conception  1      0.25   0.250    1.13 0.034  0.308  
HLA.6DRML       2      0.59   0.295    1.33 0.081  0.079 .
T1Dstatus       1      0.36   0.362    1.64 0.050  0.020 *
Residuals      22      4.88   0.222         0.668         
Total          31      7.30                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.02

Beta diversity Plot

6.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
SeqRun          3      0.71   0.235    1.07 0.096  0.308   
Nulliparous     1      0.23   0.231    1.04 0.031  0.400   
Age_LMP         1      0.28   0.283    1.28 0.039  0.128   
BMI_conception  1      0.29   0.288    1.30 0.039  0.115   
HLA.6DRML       2      0.52   0.261    1.18 0.071  0.163   
T1Dstatus       1      0.45   0.452    2.05 0.062  0.002 **
Residuals      22      4.85   0.221         0.662          
Total          31      7.34                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.002

Beta diversity Plot

6.1.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.25   0.624    4.24 0.118  0.162  
seqRun     3      1.66   0.552    3.76 0.157  0.604  
Age        1      0.47   0.475    3.23 0.045  0.859  
Parity     1      0.77   0.766    5.21 0.073  0.032 *
BMI        1      0.67   0.665    4.53 0.063  0.769  
Days       1      0.15   0.146    0.99 0.014  0.029 *
Residuals 38      5.58   0.147         0.530  0.100 .
Total     47     10.54                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

6.1.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.25   0.624    4.20 0.118   0.17  
seqRun     3      1.66   0.552    3.72 0.157   0.60  
Age        1      0.47   0.475    3.20 0.045   0.87  
Parity     1      0.77   0.766    5.16 0.073   0.03 *
BMI        1      0.67   0.665    4.48 0.063   0.78  
Tri        2      0.24   0.118    0.79 0.022   0.10  
Residuals 37      5.49   0.149         0.521   0.13  
Total     47     10.54                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

6.1.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      1.45   0.725    4.84 0.136  0.111   
seqRun     3      1.45   0.483    3.22 0.135  0.916   
Age        1      1.21   1.209    8.06 0.113  0.005 **
Parity     1      0.37   0.365    2.43 0.034  0.991   
BMI        1      0.34   0.342    2.28 0.032  0.691   
Days       1      0.18   0.184    1.23 0.017  0.013 * 
Residuals 38      5.70   0.150         0.533  0.064 . 
Total     47     10.70                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

6.1.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.45   0.725    4.73 0.136  0.126  
seqRun     3      1.45   0.483    3.15 0.135  0.923  
Age        1      1.21   1.209    7.89 0.113  0.011 *
Parity     1      0.37   0.365    2.38 0.034  0.986  
BMI        1      0.34   0.342    2.23 0.032  0.656  
Tri        2      0.21   0.106    0.69 0.020  0.417  
Residuals 37      5.67   0.153         0.530  0.153  
Total     47     10.70                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

6.1.9 Other factors

6.1.9.1 Age at conception

6.1.9.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.45   0.727    3.76 0.066  0.098 .
T1Dstatus             1      1.00   0.997    5.16 0.045  0.015 *
seqRun                3      1.49   0.498    2.57 0.067  0.599  
Tri                   2      0.25   0.126    0.65 0.011  0.466  
Age                   1      0.64   0.641    3.31 0.029  0.344  
Parity                1      0.54   0.537    2.78 0.024  0.842  
BMI                   1      0.58   0.579    2.99 0.026  0.616  
Age_Time_Interaction  1      0.14   0.143    0.74 0.006  0.132  
Residuals            83     16.04   0.193         0.725  0.025 *
Total                95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.45   0.727    3.75 0.066  0.120  
T1Dstatus             1      1.00   0.997    5.14 0.045  0.015 *
seqRun                3      1.49   0.498    2.56 0.067  0.608  
Tri                   2      0.25   0.126    0.65 0.011  0.444  
Age                   1      0.64   0.641    3.30 0.029  0.336  
Parity                1      0.54   0.537    2.77 0.024  0.855  
BMI                   1      0.58   0.579    2.98 0.026  0.621  
Age_Time_Interaction  1      0.08   0.082    0.42 0.004  0.713  
Residuals            83     16.10   0.194         0.727  0.028 *
Total                95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.45   0.727    3.75 0.066  0.094 .
T1Dstatus             1      1.00   0.997    5.15 0.045  0.011 *
seqRun                3      1.49   0.498    2.57 0.067  0.627  
Tri                   2      0.25   0.126    0.65 0.011  0.453  
Age                   1      0.64   0.641    3.31 0.029  0.351  
Parity                1      0.54   0.537    2.77 0.024  0.843  
BMI                   1      0.58   0.579    2.99 0.026  0.648  
Age_Time_Interaction  1      0.10   0.104    0.54 0.005  0.225  
Residuals            83     16.08   0.194         0.726  0.019 *
Total                95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.1.4 Age at conception (no interaction and within trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2      0.57   0.286   1.106 0.104   0.20
T1Dstatus  1      0.26   0.260   1.006 0.047   0.40
seqRun     3      0.50   0.168   0.650 0.091   0.95
Parity     1      0.32   0.321   1.242 0.058   0.53
BMI        1      0.32   0.324   1.253 0.059   0.20
Age        1      0.18   0.178   0.688 0.032   0.93
Residuals 13      3.37   0.259         0.609   0.64
Total     22      5.53                 1.000       
6.1.9.1.5 Age at conception (no interaction and within trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.76   0.382    1.97 0.087  0.110   
T1Dstatus  1      0.55   0.552    2.84 0.063  0.005 **
seqRun     3      0.84   0.279    1.44 0.095  0.927   
Parity     1      0.29   0.291    1.50 0.033  0.709   
BMI        1      0.23   0.232    1.20 0.026  0.662   
Age        1      0.31   0.307    1.58 0.035  0.286   
Residuals 30      5.83   0.194         0.661  0.027 * 
Total     39      8.81                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.1.6 Age at conception (no interaction and within trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.57   0.287   1.313 0.076  0.253   
T1Dstatus  1      0.44   0.436   1.997 0.058  0.007 **
seqRun     3      0.74   0.247   1.132 0.098  0.297   
Parity     1      0.21   0.211   0.968 0.028  0.895   
BMI        1      0.28   0.282   1.294 0.037  0.787   
Age        1      0.28   0.275   1.261 0.036  0.415   
Residuals 23      5.02   0.218         0.666  0.045 * 
Total     32      7.54                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.9.2 Body max index (BMI)

6.1.9.2.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                   2      1.45   0.727    3.75 0.066  0.117   
T1Dstatus             1      1.00   0.997    5.15 0.045  0.009 **
seqRun                3      1.49   0.498    2.57 0.067  0.614   
Tri                   2      0.25   0.126    0.65 0.011  0.489   
Age                   1      0.64   0.641    3.31 0.029  0.360   
Parity                1      0.54   0.537    2.77 0.024  0.844   
BMI                   1      0.58   0.579    2.99 0.026  0.631   
BMI_Time_Interaction  1      0.10   0.101    0.52 0.005  0.608   
Residuals            83     16.08   0.194         0.727  0.031 * 
Total                95     22.14                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.2.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.45   0.727    3.74 0.066  0.077 .
T1Dstatus             1      1.00   0.997    5.13 0.045  0.017 *
seqRun                3      1.49   0.498    2.56 0.067  0.641  
Tri                   2      0.25   0.126    0.65 0.011  0.476  
Age                   1      0.64   0.641    3.30 0.029  0.351  
Parity                1      0.54   0.537    2.77 0.024  0.810  
BMI                   1      0.58   0.579    2.98 0.026  0.626  
BMI_Time_Interaction  1      0.06   0.062    0.32 0.003  0.930  
Residuals            83     16.12   0.194         0.728  0.024 *
Total                95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.2.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.45   0.727    3.75 0.066  0.093 .
T1Dstatus             1      1.00   0.997    5.15 0.045  0.013 *
seqRun                3      1.49   0.498    2.57 0.067  0.615  
Tri                   2      0.25   0.126    0.65 0.011  0.473  
Age                   1      0.64   0.641    3.31 0.029  0.336  
Parity                1      0.54   0.537    2.77 0.024  0.826  
BMI                   1      0.58   0.579    2.99 0.026  0.599  
BMI_Time_Interaction  1      0.10   0.104    0.54 0.005  0.054 .
Residuals            83     16.08   0.194         0.726  0.018 *
Total                95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.2.4 BMI (no interaction but within T1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2      0.57   0.286   1.155 0.104   0.23
T1Dstatus  1      0.26   0.260   1.051 0.047   0.41
seqRun     1      0.22   0.215   0.869 0.039   0.73
Age        1      0.23   0.233   0.939 0.042   0.89
Parity     1      0.29   0.286   1.153 0.052   0.72
BMI        1      0.24   0.243   0.981 0.044   0.67
Residuals 15      3.72   0.248         0.673   0.59
Total     22      5.53                 1.000       
6.1.9.2.5 BMI (no interaction but within T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.76   0.382    1.92 0.087  0.095 . 
T1Dstatus  1      0.55   0.552    2.77 0.063  0.008 **
seqRun     1      0.32   0.321    1.61 0.036  0.939   
Age        1      0.29   0.294    1.48 0.033  0.285   
Parity     1      0.29   0.293    1.47 0.033  0.713   
BMI        1      0.22   0.217    1.09 0.025  0.536   
Residuals 32      6.37   0.199         0.723  0.014 * 
Total     39      8.81                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.2.6 BMI (no interaction but within T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.57   0.287    1.29 0.076  0.212   
T1Dstatus  1      0.44   0.436    1.97 0.058  0.010 **
seqRun     1      0.24   0.243    1.09 0.032  0.065 . 
Age        1      0.29   0.292    1.32 0.039  0.366   
Parity     1      0.21   0.206    0.93 0.027  0.914   
BMI        1      0.24   0.245    1.10 0.032  0.810   
Residuals 25      5.54   0.222         0.735  0.031 * 
Total     32      7.54                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.9.3 HLA type

6.1.9.3.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.45   0.727    3.77 0.066  0.096 .
T1Dstatus             1      1.00   0.997    5.18 0.045  0.014 *
Days                  1      0.15   0.148    0.77 0.007  0.127  
seqRun                3      1.49   0.496    2.57 0.067  0.611  
Age                   1      0.63   0.629    3.26 0.028  0.412  
Parity                1      0.54   0.544    2.82 0.025  0.836  
BMI                   1      0.57   0.569    2.95 0.026  0.659  
HLA_Time_Interaction  1      0.12   0.123    0.64 0.006  1.000  
Residuals            84     16.18   0.193         0.731  0.466  
Total                95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.3.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                   2      1.45   0.727    3.77 0.066  0.094 . 
T1Dstatus             1      1.00   0.997    5.18 0.045  0.010 **
Days                  1      0.15   0.148    0.77 0.007  0.146   
seqRun                3      1.49   0.496    2.57 0.067  0.629   
Age                   1      0.63   0.629    3.26 0.028  0.413   
Parity                1      0.54   0.544    2.82 0.025  0.827   
BMI                   1      0.57   0.569    2.95 0.026  0.649   
HLA_Time_Interaction  1      0.12   0.119    0.61 0.005  1.000   
Residuals            84     16.19   0.193         0.731  0.180   
Total                95     22.14                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.3.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.45   0.727    3.77 0.066  0.083 .
T1Dstatus             1      1.00   0.997    5.18 0.045  0.014 *
Days                  1      0.15   0.148    0.77 0.007  0.131  
seqRun                3      1.49   0.496    2.58 0.067  0.649  
Age                   1      0.63   0.629    3.27 0.028  0.412  
Parity                1      0.54   0.544    2.82 0.025  0.821  
BMI                   1      0.57   0.569    2.96 0.026  0.689  
HLA_Time_Interaction  1      0.14   0.135    0.70 0.006  1.000  
Residuals            84     16.17   0.193         0.731  0.200  
Total                95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.3.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1      0.16   0.158    0.82 0.007  0.115  
seqRun     3      1.51   0.503    2.62 0.068  0.528  
Age        1      0.61   0.613    3.20 0.028  0.950  
Parity     1      0.61   0.608    3.17 0.027  0.054 .
BMI        1      0.59   0.592    3.08 0.027  0.778  
T1Dstatus  1      0.80   0.798    4.16 0.036  0.100 .
HLA        2      1.55   0.775    4.04 0.070  0.051 .
Residuals 85     16.31   0.192         0.737  0.016 *
Total     95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.9.4 Parity

6.1.9.4.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      1.45   0.727    3.78 0.066  0.078 .
T1Dstatus                1      1.00   0.997    5.18 0.045  0.019 *
Days                     1      0.15   0.148    0.77 0.007  0.134  
seqRun                   3      1.49   0.496    2.58 0.067  0.644  
Age                      1      0.63   0.629    3.27 0.028  0.408  
Parity                   1      0.54   0.544    2.83 0.025  0.835  
BMI                      1      0.57   0.569    2.96 0.026  0.672  
Parity_Time_Interaction  1      0.14   0.143    0.74 0.006  0.050 *
Residuals               84     16.16   0.192         0.730  0.014 *
Total                   95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.4.2 Parity (no interaction but within T1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2      0.57   0.286   1.155 0.104   0.21
T1Dstatus  1      0.26   0.260   1.051 0.047   0.40
seqRun     1      0.22   0.215   0.869 0.039   0.75
Age        1      0.23   0.233   0.939 0.042   0.86
BMI        1      0.25   0.254   1.026 0.046   0.85
Parity     1      0.27   0.275   1.107 0.050   0.45
Residuals 15      3.72   0.248         0.673   0.58
Total     22      5.53                 1.000       
6.1.9.4.3 Parity (no interaction but within T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.76   0.382    1.92 0.087  0.092 . 
T1Dstatus  1      0.55   0.552    2.77 0.063  0.005 **
seqRun     1      0.32   0.321    1.61 0.036  0.915   
Age        1      0.29   0.294    1.48 0.033  0.315   
BMI        1      0.30   0.303    1.52 0.034  0.451   
Parity     1      0.21   0.208    1.04 0.024  0.812   
Residuals 32      6.37   0.199         0.723  0.014 * 
Total     39      8.81                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.4.4 Parity (no interaction but within T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.57   0.287    1.29 0.076  0.219   
T1Dstatus  1      0.44   0.436    1.97 0.058  0.010 **
seqRun     1      0.24   0.243    1.09 0.032  0.061 . 
Age        1      0.29   0.292    1.32 0.039  0.355   
BMI        1      0.23   0.227    1.02 0.030  0.661   
Parity     1      0.22   0.224    1.01 0.030  0.918   
Residuals 25      5.54   0.222         0.735  0.026 * 
Total     32      7.54                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.9.5 Mode of delivery

6.1.9.5.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.45   0.727    4.01 0.066  0.099 .
T1Dstatus             1      1.00   0.997    5.51 0.045  0.022 *
MOD                   2      1.11   0.555    3.06 0.050  0.573  
Days                  1      0.15   0.148    0.82 0.007  0.117  
seqRun                3      1.54   0.512    2.83 0.069  0.471  
Age                   1      0.76   0.762    4.21 0.034  0.059 .
Parity                1      0.51   0.515    2.84 0.023  0.840  
BMI                   1      0.62   0.622    3.43 0.028  0.406  
MOD_Time_Interaction  1      0.15   0.145    0.80 0.007  1.000  
Residuals            82     14.85   0.181         0.671  0.184  
Total                95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.5.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.45   0.727    4.00 0.066  0.106  
T1Dstatus             1      1.00   0.997    5.49 0.045  0.012 *
MOD                   2      1.11   0.555    3.05 0.050  0.537  
Days                  1      0.15   0.148    0.82 0.007  0.100 .
seqRun                3      1.54   0.512    2.82 0.069  0.457  
Age                   1      0.76   0.762    4.19 0.034  0.056 .
Parity                1      0.51   0.515    2.83 0.023  0.840  
BMI                   1      0.62   0.622    3.42 0.028  0.388  
MOD_Time_Interaction  1      0.08   0.085    0.47 0.004  1.000  
Residuals            82     14.91   0.182         0.673  0.092 .
Total                95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.5.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                   2      1.45   0.727    4.00 0.066  0.092 . 
T1Dstatus             1      1.00   0.997    5.49 0.045  0.009 **
MOD                   2      1.11   0.555    3.05 0.050  0.559   
Days                  1      0.15   0.148    0.82 0.007  0.116   
seqRun                3      1.54   0.512    2.82 0.069  0.470   
Age                   1      0.76   0.762    4.19 0.034  0.051 . 
Parity                1      0.51   0.515    2.83 0.023  0.864   
BMI                   1      0.62   0.622    3.42 0.028  0.364   
MOD_Time_Interaction  1      0.10   0.100    0.55 0.005  1.000   
Residuals            82     14.89   0.182         0.673  0.149   
Total                95     22.14                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.5.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days       1      0.16   0.158    0.87 0.007  0.100 . 
seqRun     3      1.51   0.503    2.79 0.068  0.572   
Age        1      0.61   0.613    3.39 0.028  0.958   
Parity     1      0.61   0.608    3.37 0.027  0.058 . 
BMI        1      0.59   0.592    3.28 0.027  0.806   
HLA        2      1.38   0.690    3.82 0.062  0.171   
T1Dstatus  1      0.97   0.968    5.36 0.044  0.025 * 
MOD        2      1.31   0.657    3.64 0.059  0.209   
Residuals 83     14.99   0.181         0.677  0.009 **
Total     95     22.14                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.9.6 Carbohydrate intake

6.1.9.6.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.45   0.727    3.80 0.066  0.092 .
T1Dstatus              1      1.00   0.997    5.21 0.045  0.014 *
Carbs                  1      0.45   0.453    2.36 0.020  0.782  
seqRun                 3      1.49   0.496    2.59 0.067  0.638  
Tri                    2      0.25   0.123    0.64 0.011  0.500  
Age                    1      0.59   0.588    3.07 0.027  0.661  
Parity                 1      0.51   0.514    2.68 0.023  0.889  
BMI                    1      0.59   0.587    3.07 0.027  0.542  
Carb_Time_Interaction  1      0.11   0.114    0.60 0.005  0.949  
Residuals             82     15.70   0.191         0.709  0.144  
Total                 95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.6.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.45   0.727    3.78 0.066   0.11   
T1Dstatus              1      1.00   0.997    5.19 0.045   0.01 **
Carbs                  1      0.45   0.453    2.35 0.020   0.79   
seqRun                 3      1.49   0.496    2.58 0.067   0.65   
Tri                    2      0.25   0.123    0.64 0.011   0.51   
Age                    1      0.59   0.588    3.06 0.027   0.62   
Parity                 1      0.51   0.514    2.67 0.023   0.88   
BMI                    1      0.59   0.587    3.05 0.027   0.54   
Carb_Time_Interaction  1      0.04   0.042    0.22 0.002   1.00   
Residuals             82     15.77   0.192         0.712   0.22   
Total                 95     22.14                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.6.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.45   0.727    3.79 0.066   0.10   
T1Dstatus              1      1.00   0.997    5.20 0.045   0.01 **
Carbs                  1      0.45   0.453    2.36 0.020   0.80   
seqRun                 3      1.49   0.496    2.59 0.067   0.66   
Tri                    2      0.25   0.123    0.64 0.011   0.48   
Age                    1      0.59   0.588    3.07 0.027   0.65   
Parity                 1      0.51   0.514    2.68 0.023   0.87   
BMI                    1      0.59   0.587    3.06 0.027   0.55   
Carb_Time_Interaction  1      0.08   0.085    0.44 0.004   0.99   
Residuals             82     15.73   0.192         0.710   0.13   
Total                 95     22.14                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.6.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun     3      1.52   0.506    2.66 0.069  0.147  
Tri        2      0.27   0.134    0.70 0.012  0.477  
Age        1      0.63   0.625    3.28 0.028  0.574  
Parity     1      0.61   0.607    3.18 0.027  0.155  
BMI        1      0.59   0.595    3.12 0.027  0.777  
HLA        2      1.36   0.682    3.58 0.062  0.161  
T1Dstatus  1      0.98   0.976    5.12 0.044  0.018 *
Carbs      1      0.37   0.374    1.96 0.017  0.919  
Residuals 83     15.81   0.190         0.714  0.105  
Total     95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.9.7 Fibre intake

6.1.9.7.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      1.45   0.727    3.79 0.066  0.083 .
T1Dstatus               1      1.00   0.997    5.20 0.045  0.019 *
Fiber                   1      0.39   0.389    2.03 0.018  0.908  
seqRun                  3      1.47   0.490    2.55 0.066  0.725  
Tri                     2      0.25   0.126    0.66 0.011  0.432  
Age                     1      0.60   0.600    3.13 0.027  0.552  
Parity                  1      0.52   0.523    2.73 0.024  0.844  
BMI                     1      0.60   0.600    3.13 0.027  0.479  
Fiber_Time_Interaction  1      0.11   0.111    0.58 0.005  0.888  
Residuals              82     15.74   0.192         0.711  0.145  
Total                  95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.7.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      1.45   0.727    3.77 0.066  0.087 .
T1Dstatus               1      1.00   0.997    5.17 0.045  0.012 *
Fiber                   1      0.39   0.389    2.02 0.018  0.930  
seqRun                  3      1.47   0.490    2.54 0.066  0.707  
Tri                     2      0.25   0.126    0.66 0.011  0.403  
Age                     1      0.60   0.600    3.11 0.027  0.599  
Parity                  1      0.52   0.523    2.71 0.024  0.845  
BMI                     1      0.60   0.600    3.11 0.027  0.477  
Fiber_Time_Interaction  1      0.04   0.043    0.22 0.002  1.000  
Residuals              82     15.81   0.193         0.714  0.227  
Total                  95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.7.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      1.45   0.727    3.78 0.066  0.105  
T1Dstatus               1      1.00   0.997    5.19 0.045  0.015 *
Fiber                   1      0.39   0.389    2.03 0.018  0.913  
seqRun                  3      1.47   0.490    2.55 0.066  0.697  
Tri                     2      0.25   0.126    0.66 0.011  0.441  
Age                     1      0.60   0.600    3.12 0.027  0.565  
Parity                  1      0.52   0.523    2.72 0.024  0.849  
BMI                     1      0.60   0.600    3.12 0.027  0.488  
Fiber_Time_Interaction  1      0.09   0.089    0.46 0.004  0.959  
Residuals              82     15.76   0.192         0.712  0.142  
Total                  95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.7.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun     3      1.52   0.506    2.65 0.069  0.152  
Tri        2      0.27   0.134    0.70 0.012  0.468  
Age        1      0.63   0.625    3.27 0.028  0.558  
Parity     1      0.61   0.607    3.18 0.027  0.151  
BMI        1      0.59   0.595    3.11 0.027  0.786  
HLA        2      1.36   0.682    3.57 0.062  0.182  
T1Dstatus  1      0.98   0.976    5.11 0.044  0.022 *
Fiber      1      0.33   0.334    1.75 0.015  0.961  
Residuals 83     15.85   0.191         0.716  0.126  
Total     95     22.14                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.9.8 1,5-AG (glucose control measurement)

6.1.9.8.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      1.54   0.771    4.18 0.073  0.066 .
T1Dstatus             1      1.01   1.013    5.49 0.048  0.013 *
Days                  1      0.14   0.143    0.78 0.007  0.314  
seqRun                3      1.40   0.468    2.54 0.067  0.767  
Age                   1      0.67   0.674    3.66 0.032  0.259  
Parity                1      0.56   0.556    3.01 0.026  0.779  
BMI                   1      0.51   0.512    2.77 0.024  0.743  
AG15                  1      0.59   0.595    3.22 0.028  0.020 *
AG15_T1D_Interaction  1      0.34   0.340    1.84 0.016  0.979  
Residuals            77     14.21   0.184         0.677  0.011 *
Total                89     20.98                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.8.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.27   0.634    4.51 0.135  0.138  
Days       1      0.23   0.233    1.66 0.025  0.020 *
seqRun     3      1.45   0.482    3.43 0.154  0.943  
Age        1      0.39   0.387    2.75 0.041  0.936  
Parity     1      0.79   0.790    5.62 0.084  0.018 *
BMI        1      0.64   0.639    4.54 0.068  0.677  
AG15       1      0.24   0.241    1.72 0.026  0.963  
Residuals 31      4.36   0.141         0.466  0.443  
Total     41      9.37                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.9.8.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      1.45   0.725    5.14 0.136  0.115   
Days       1      0.18   0.181    1.28 0.017  0.028 * 
seqRun     3      1.45   0.483    3.42 0.136  0.942   
Age        1      1.21   1.209    8.57 0.113  0.010 **
Parity     1      0.37   0.374    2.65 0.035  0.987   
BMI        1      0.34   0.335    2.38 0.031  0.727   
AG15       1      0.48   0.478    3.39 0.045  0.858   
Residuals 37      5.22   0.141         0.488  0.153   
Total     47     10.70                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.2 Differential abundance analysis Strain taxonomic level

Controlling for multiple measurements, sequencing run, conception age, BMI, parity and HLA type

       nonT1D_vs_T1D  T1  T2  T3 T1_vs_T2 T2_vs_T3 T1_vs_T3 T1DT1vsT2 T1DT2vsT3 T1DT1vsT3
Down               0   0   0   0        0        0        0         0         0         0
NotSig           267 267 267 267      267      267       71       267       267        76
Up                 0   0   0   0        0        0      196         0         0       191
       noT1DT1vsT2 noT1DT2vsT3 noT1DT1vsT3
Down             0           0           0
NotSig         267         267         266
Up               0           0           1

6.2.1 Across all trimesters (T1D vs non-T1D)

[1] "No DA taxa found"

6.2.2 Only Trimester 1 (nonT1D vs T1D)

[1] "No DA taxa found"

6.2.3 Only Trimester 2 (nonT1D vs T1D)

[1] "No DA taxa found"

6.2.4 Only Trimester 3 (nonT1D vs T1D)

[1] "No DA taxa found"

6.2.5 T1 vs T2 (All data)

                                           Classification LogFC   P.Val adj.P.Val
1 Eubacterium_siraeum_St_Eubacterium_siraeum_unclassified 0.583 0.04450    0.0720
2                    Ruminococcus_bromii_St_GCF_000209875 0.517 0.00724    0.0671
  T1:mean% T1Prev% T2:mean% T2Prev% T3:mean% T3Prev%
1     5.78     100     4.31     100     2.51     100
2     1.52     100     1.63     100     1.05      97

6.2.6 T2 vs T3 (All data)

[1] "No DA taxa"

6.2.7 T1 vs T3 (All data)

                                                         Classification LogFC    P.Val
1               Eubacterium_siraeum_St_Eubacterium_siraeum_unclassified 0.816 5.52e-03
2                                  Ruminococcus_bromii_St_GCF_000209875 0.767 9.92e-05
3 Haemophilus_parainfluenzae_St_Haemophilus_parainfluenzae_unclassified 0.599 7.98e-06
  adj.P.Val T1:mean% T1Prev% T2:mean% T2Prev% T3:mean% T3Prev%
1   0.02084    5.776   100.0    4.306     100    2.513   100.0
2   0.00883    1.519   100.0    1.629     100    1.047    97.0
3   0.00213    0.201    78.3    0.111      75    0.052    48.5

No differentially abundant strains were detected between T1D and non-T1D women accross trimesters or in each trimesters separatelly (i.e. nonT1D_vs_T1D, T1, T2 and T3 contrasts had no strains up or down). In addition no differences between T1 and T2 (i.e. contrast T1_vs_T2) and between T2 and T3 (contrast T2_vs_T3) were found when samples from T1D and non-T1D women were assessed together. In T1D women only and in non-T1D women only, significant differences were detected only between trimesters 1 and 3 (i.e. T1DT1vsT3 and noT1DT1vsT3, respectively)

Results for contrasts with significant differentially abundant strains shown below

6.2.8 T1 vs T2 (in women with T1D)

                                                     Classification  LogFC    P.Val
2 Bacteroides_massiliensis_St_Bacteroides_massiliensis_unclassified -0.558 0.042732
3              Lachnospiraceae_bacterium_8_1_57FAA_St_GCF_000185545  0.509 0.001732
1                          Collinsella_aerofaciens_St_GCF_000169035  0.522 0.019438
5                          Akkermansia_muciniphila_St_GCF_000020225  0.708 0.042569
4                              Ruminococcus_bromii_St_GCF_000209875  0.893 0.000859
  adj.P.Val T1:mean% T1Prev% T2:mean% T2Prev%
2    0.0872    0.282     100    1.852     100
3    0.0872    0.096      50    0.049      45
1    0.0872    0.998      75    0.799      85
5    0.0872    3.384     100    1.331     100
4    0.0817    1.647     100    0.867     100
[1] 5

6.2.9 T2 vs T3 (in women with T1D)

[1] Classification LogFC          P.Val          adj.P.Val      T2:mean%      
[6] T2Prev%        T3:mean%       T3Prev%       
<0 rows> (or 0-length row.names)

6.2.10 T1 vs T3 (in women with T1D)

                                                             Classification LogFC
7             Oxalobacter_formigenes_St_Oxalobacter_formigenes_unclassified 0.537
4                      Lachnospiraceae_bacterium_8_1_57FAA_St_GCF_000185545 0.579
2   Parabacteroides_goldsteinii_St_Parabacteroides_goldsteinii_unclassified 0.595
1 Bifidobacterium_adolescentis_St_Bifidobacterium_adolescentis_unclassified 0.612
5             Roseburia_intestinalis_St_Roseburia_intestinalis_unclassified 0.692
3                   Eubacterium_siraeum_St_Eubacterium_siraeum_unclassified 0.713
8                                  Akkermansia_muciniphila_St_GCF_000020225 0.967
6                                      Ruminococcus_bromii_St_GCF_000209875 1.228
     P.Val adj.P.Val T1:mean% T1Prev% T3:mean% T3Prev%
7 5.96e-04   0.03976    0.079    58.3    0.010    50.0
4 4.25e-04   0.03779    0.096    50.0    0.036    37.5
2 1.87e-03   0.04082    0.665    41.7    0.403    56.2
1 1.88e-02   0.04082    0.633    75.0    0.083    81.2
5 3.19e-03   0.04082    0.590    66.7    0.118    68.8
3 7.73e-02   0.09252    1.798   100.0    2.428   100.0
8 6.74e-03   0.04082    3.384   100.0    1.031   100.0
6 8.30e-06   0.00222    1.647   100.0    0.305   100.0
[1] 13

6.2.11 T1 vs T2 (in women without T1D)

[1] "No DA taxa found"

6.2.12 T2 vs T3 (in women without T1D)

[1] "No DA taxa found"

6.2.13 T1 vs T3 (in women without T1D)

                                                         Classification LogFC    P.Val
1 Haemophilus_parainfluenzae_St_Haemophilus_parainfluenzae_unclassified 0.718 0.000169
2 Haemophilus_parainfluenzae_St_Haemophilus_parainfluenzae_unclassified 0.718 0.000169
  adj.P.Val mean% Prev%
1    0.0452 0.189  90.9
2    0.0452 0.052  52.9
[1] 14

7 Genus taxonomic level

7.1 Microbial community composition analysis at Genus level (Beta diversity analysis)

7.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
seqRun                3      0.74   0.247    2.68 0.069  0.018 * 
Days                  1      0.11   0.109    1.18 0.010  0.090 . 
T1D_Time_Interaction  1      0.51   0.513    5.55 0.048  0.006 **
Age                   1      0.42   0.420    4.55 0.039  0.995   
Parity                1      0.26   0.259    2.81 0.024  0.009 **
BMI                   1      0.28   0.279    3.02 0.026  0.994   
HLA                   2      0.54   0.270    2.92 0.050  0.315   
T1Dstatus             1      0.12   0.118    1.27 0.011  0.913   
Residuals            84      7.76   0.092         0.723  0.353   
Total                95     10.74                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.006

7.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3     0.275  0.0918   0.756 0.102   0.81
Nulliparous     1     0.154  0.1537   1.265 0.057   0.26
Age_LMP         1     0.170  0.1705   1.403 0.063   0.17
BMI_conception  1     0.132  0.1322   1.089 0.049   0.38
HLA.6DRML       2     0.208  0.1041   0.857 0.077   0.62
T1Dstatus       1     0.179  0.1792   1.475 0.066   0.15
Residuals      13     1.579  0.1215         0.585       
Total          22     2.698                 1.000       
[1] 0.152

Beta diversity Plot

7.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3      0.40  0.1325    1.18 0.109   0.27
Nulliparous     1      0.08  0.0841    0.75 0.023   0.64
Age_LMP         1      0.17  0.1666    1.49 0.046   0.16
BMI_conception  1      0.15  0.1462    1.30 0.040   0.22
HLA.6DRML       2      0.24  0.1191    1.06 0.065   0.37
T1Dstatus       1      0.14  0.1374    1.23 0.038   0.28
Residuals      22      2.47  0.1122         0.678       
Total          31      3.64                 1.000       
[1] 0.279

Beta diversity Plot

7.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3      0.29  0.0970   0.932 0.082  0.560  
Nulliparous     1      0.14  0.1427   1.370 0.040  0.180  
Age_LMP         1      0.16  0.1557   1.495 0.044  0.137  
BMI_conception  1      0.22  0.2192   2.105 0.062  0.047 *
HLA.6DRML       2      0.16  0.0809   0.777 0.046  0.730  
T1Dstatus       1      0.29  0.2879   2.765 0.081  0.015 *
Residuals      22      2.29  0.1041         0.645         
Total          31      3.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.015

Beta diversity Plot

7.1.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.32   0.160    2.52 0.069  0.698  
seqRun     3      0.75   0.251    3.95 0.163  0.608  
Age        1      0.37   0.375    5.90 0.081  0.354  
Parity     1      0.36   0.363    5.73 0.079  0.014 *
BMI        1      0.27   0.272    4.28 0.059  0.820  
Days       1      0.12   0.122    1.93 0.026  0.021 *
Residuals 38      2.41   0.063         0.523  0.190  
Total     47      4.62                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

7.1.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.32   0.160    2.48 0.069  0.728  
seqRun     3      0.75   0.251    3.89 0.163  0.551  
Age        1      0.37   0.375    5.81 0.081  0.356  
Parity     1      0.36   0.363    5.63 0.079  0.016 *
BMI        1      0.27   0.272    4.22 0.059  0.772  
Tri        2      0.15   0.074    1.15 0.032  0.115  
Residuals 37      2.39   0.065         0.517  0.241  
Total     47      4.62                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

7.1.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.68   0.342    4.15 0.121  0.241  
seqRun     3      0.58   0.193    2.34 0.103  0.902  
Age        1      0.78   0.783    9.50 0.139  0.066 .
Parity     1      0.13   0.129    1.57 0.023  0.970  
BMI        1      0.21   0.210    2.55 0.037  0.474  
Days       1      0.13   0.130    1.58 0.023  0.035 *
Residuals 38      3.13   0.082         0.554  0.186  
Total     47      5.64                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

7.1.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.68   0.342    4.06 0.121  0.210  
seqRun     3      0.58   0.193    2.29 0.103  0.915  
Age        1      0.78   0.783    9.28 0.139  0.052 .
Parity     1      0.13   0.129    1.53 0.023  0.976  
BMI        1      0.21   0.210    2.49 0.037  0.469  
Tri        2      0.14   0.070    0.83 0.025  0.320  
Residuals 37      3.12   0.084         0.553  0.234  
Total     47      5.64                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

7.1.9 Other factors

7.1.9.1 Age at conception

7.1.9.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.46 0.044  0.616  
T1Dstatus             1      0.56   0.564    5.95 0.053  0.025 *
seqRun                3      0.69   0.231    2.43 0.064  0.699  
Tri                   2      0.11   0.056    0.60 0.011  0.610  
Age                   1      0.43   0.426    4.49 0.040  0.275  
Parity                1      0.24   0.237    2.50 0.022  0.736  
BMI                   1      0.31   0.308    3.25 0.029  0.739  
Age_Time_Interaction  1      0.05   0.054    0.56 0.005  0.581  
Residuals            83      7.87   0.095         0.733  0.255  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.45 0.044  0.602  
T1Dstatus             1      0.56   0.564    5.92 0.053  0.031 *
seqRun                3      0.69   0.231    2.42 0.064  0.694  
Tri                   2      0.11   0.056    0.59 0.011  0.636  
Age                   1      0.43   0.426    4.47 0.040  0.297  
Parity                1      0.24   0.237    2.49 0.022  0.702  
BMI                   1      0.31   0.308    3.23 0.029  0.715  
Age_Time_Interaction  1      0.01   0.011    0.11 0.001  0.984  
Residuals            83      7.92   0.095         0.737  0.320  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.46 0.044  0.594  
T1Dstatus             1      0.56   0.564    5.94 0.053  0.026 *
seqRun                3      0.69   0.231    2.43 0.064  0.668  
Tri                   2      0.11   0.056    0.59 0.011  0.596  
Age                   1      0.43   0.426    4.49 0.040  0.315  
Parity                1      0.24   0.237    2.50 0.022  0.713  
BMI                   1      0.31   0.308    3.24 0.029  0.750  
Age_Time_Interaction  1      0.04   0.037    0.39 0.003  0.703  
Residuals            83      7.89   0.095         0.735  0.250  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.1.4 Age at conception (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.47   0.234    2.48 0.044  0.574  
T1Dstatus  1      0.56   0.564    5.98 0.053  0.029 *
seqRun     3      0.69   0.231    2.44 0.064  0.684  
Tri        2      0.11   0.056    0.60 0.011  0.599  
Parity     1      0.21   0.212    2.25 0.020  0.800  
BMI        1      0.36   0.363    3.84 0.034  0.582  
Age        1      0.40   0.397    4.21 0.037  0.434  
Residuals 84      7.93   0.094         0.738  0.211  
Total     95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.2 Body max index (BMI)

7.1.9.2.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.46 0.044  0.621  
T1Dstatus             1      0.56   0.564    5.93 0.053  0.028 *
seqRun                3      0.69   0.231    2.43 0.064  0.672  
Tri                   2      0.11   0.056    0.59 0.011  0.635  
Age                   1      0.43   0.426    4.48 0.040  0.283  
Parity                1      0.24   0.237    2.50 0.022  0.690  
BMI                   1      0.31   0.308    3.24 0.029  0.742  
BMI_Time_Interaction  1      0.03   0.031    0.32 0.003  0.883  
Residuals            83      7.90   0.095         0.736  0.268  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.2.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.45 0.044  0.573  
T1Dstatus             1      0.56   0.564    5.92 0.053  0.027 *
seqRun                3      0.69   0.231    2.42 0.064  0.672  
Tri                   2      0.11   0.056    0.59 0.011  0.620  
Age                   1      0.43   0.426    4.48 0.040  0.317  
Parity                1      0.24   0.237    2.49 0.022  0.721  
BMI                   1      0.31   0.308    3.24 0.029  0.746  
BMI_Time_Interaction  1      0.02   0.020    0.21 0.002  0.917  
Residuals            83      7.91   0.095         0.736  0.278  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.2.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.46 0.044  0.581  
T1Dstatus             1      0.56   0.564    5.94 0.053  0.031 *
seqRun                3      0.69   0.231    2.43 0.064  0.677  
Tri                   2      0.11   0.056    0.59 0.011  0.617  
Age                   1      0.43   0.426    4.49 0.040  0.286  
Parity                1      0.24   0.237    2.50 0.022  0.696  
BMI                   1      0.31   0.308    3.25 0.029  0.733  
BMI_Time_Interaction  1      0.05   0.046    0.49 0.004  0.378  
Residuals            83      7.88   0.095         0.734  0.215  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.2.4 BMI (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.47   0.234    2.48 0.044  0.589  
T1Dstatus  1      0.56   0.564    5.98 0.053  0.025 *
seqRun     3      0.69   0.231    2.44 0.064  0.684  
Tri        2      0.11   0.056    0.60 0.011  0.611  
Age        1      0.43   0.426    4.52 0.040  0.264  
Parity     1      0.24   0.237    2.52 0.022  0.704  
BMI        1      0.31   0.308    3.27 0.029  0.745  
Residuals 84      7.93   0.094         0.738  0.213  
Total     95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.3 HLA type

7.1.9.3.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.48 0.044  0.609  
T1Dstatus             1      0.56   0.564    6.00 0.053  0.030 *
Days                  1      0.12   0.117    1.24 0.011  0.088 .
seqRun                3      0.68   0.227    2.42 0.064  0.703  
Age                   1      0.41   0.413    4.39 0.039  0.369  
Parity                1      0.24   0.236    2.51 0.022  0.715  
BMI                   1      0.30   0.302    3.21 0.028  0.766  
HLA_Time_Interaction  1      0.05   0.048    0.51 0.004  1.000  
Residuals            84      7.91   0.094         0.736  0.564  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.3.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.49 0.044  0.587  
T1Dstatus             1      0.56   0.564    6.01 0.053  0.023 *
Days                  1      0.12   0.117    1.24 0.011  0.082 .
seqRun                3      0.68   0.227    2.42 0.064  0.717  
Age                   1      0.41   0.413    4.40 0.039  0.373  
Parity                1      0.24   0.236    2.51 0.022  0.738  
BMI                   1      0.30   0.302    3.21 0.028  0.795  
HLA_Time_Interaction  1      0.06   0.064    0.68 0.006  0.998  
Residuals            84      7.89   0.094         0.735  0.324  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.3.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.49 0.044  0.579  
T1Dstatus             1      0.56   0.564    6.01 0.053  0.035 *
Days                  1      0.12   0.117    1.24 0.011  0.082 .
seqRun                3      0.68   0.227    2.42 0.064  0.702  
Age                   1      0.41   0.413    4.40 0.039  0.350  
Parity                1      0.24   0.236    2.51 0.022  0.722  
BMI                   1      0.30   0.302    3.21 0.028  0.783  
HLA_Time_Interaction  1      0.06   0.060    0.64 0.006  0.955  
Residuals            84      7.89   0.094         0.735  0.226  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.3.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days       1      0.12   0.121    1.30 0.011  0.102   
seqRun     3      0.73   0.243    2.60 0.068  0.728   
Age        1      0.39   0.391    4.18 0.036  0.994   
Parity     1      0.27   0.271    2.90 0.025  0.003 **
BMI        1      0.35   0.354    3.79 0.033  0.897   
T1Dstatus  1      0.39   0.393    4.20 0.037  0.120   
HLA        2      0.52   0.261    2.79 0.049  0.407   
Residuals 85      7.95   0.094         0.741  0.184   
Total     95     10.74                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.4 Parity

7.1.9.4.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.47   0.234    2.49 0.044  0.586  
T1Dstatus                1      0.56   0.564    6.02 0.053  0.028 *
Days                     1      0.12   0.117    1.24 0.011  0.088 .
seqRun                   3      0.68   0.227    2.43 0.064  0.684  
Age                      1      0.41   0.413    4.41 0.039  0.340  
Parity                   1      0.24   0.236    2.52 0.022  0.732  
BMI                      1      0.30   0.302    3.22 0.028  0.788  
Parity_Time_Interaction  1      0.08   0.076    0.81 0.007  0.157  
Residuals               84      7.88   0.094         0.734  0.131  
Total                   95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.4.2 Parity (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.47   0.234    2.50 0.044  0.577  
T1Dstatus  1      0.56   0.564    6.03 0.053  0.031 *
Days       1      0.12   0.117    1.25 0.011  0.096 .
seqRun     3      0.68   0.227    2.43 0.064  0.669  
BMI        1      0.44   0.444    4.75 0.041  0.394  
Age        1      0.37   0.375    4.01 0.035  0.451  
Parity     1      0.13   0.132    1.41 0.012  0.942  
Residuals 85      7.95   0.094         0.741  0.176  
Total     95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.5 Mode of delivery

7.1.9.5.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.61 0.044  0.580  
T1Dstatus             1      0.56   0.564    6.31 0.053  0.015 *
MOD                   2      0.32   0.159    1.78 0.030  0.906  
Days                  1      0.12   0.119    1.33 0.011  0.095 .
seqRun                3      0.73   0.244    2.73 0.068  0.440  
Age                   1      0.59   0.592    6.62 0.055  0.013 *
Parity                1      0.22   0.222    2.48 0.021  0.765  
BMI                   1      0.31   0.310    3.47 0.029  0.662  
MOD_Time_Interaction  1      0.07   0.074    0.83 0.007  0.988  
Residuals            82      7.34   0.089         0.683  0.292  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.5.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.61 0.044  0.597  
T1Dstatus             1      0.56   0.564    6.30 0.053  0.018 *
MOD                   2      0.32   0.159    1.77 0.030  0.896  
Days                  1      0.12   0.119    1.32 0.011  0.088 .
seqRun                3      0.73   0.244    2.73 0.068  0.429  
Age                   1      0.59   0.592    6.61 0.055  0.015 *
Parity                1      0.22   0.222    2.48 0.021  0.747  
BMI                   1      0.31   0.310    3.46 0.029  0.655  
MOD_Time_Interaction  1      0.07   0.067    0.75 0.006  0.998  
Residuals            82      7.34   0.090         0.684  0.390  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.5.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.47   0.234    2.61 0.044  0.593  
T1Dstatus             1      0.56   0.564    6.30 0.053  0.041 *
MOD                   2      0.32   0.159    1.77 0.030  0.896  
Days                  1      0.12   0.119    1.32 0.011  0.080 .
seqRun                3      0.73   0.244    2.73 0.068  0.470  
Age                   1      0.59   0.592    6.61 0.055  0.018 *
Parity                1      0.22   0.222    2.48 0.021  0.755  
BMI                   1      0.31   0.310    3.46 0.029  0.640  
MOD_Time_Interaction  1      0.07   0.066    0.74 0.006  0.997  
Residuals            82      7.34   0.090         0.684  0.492  
Total                95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.5.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days       1      0.12   0.121    1.36 0.011  0.081 . 
seqRun     3      0.73   0.243    2.72 0.068  0.707   
Age        1      0.39   0.391    4.38 0.036  0.996   
Parity     1      0.27   0.271    3.04 0.025  0.004 **
BMI        1      0.35   0.354    3.97 0.033  0.905   
HLA        2      0.45   0.227    2.54 0.042  0.529   
T1Dstatus  1      0.46   0.461    5.17 0.043  0.075 . 
MOD        2      0.54   0.272    3.04 0.051  0.345   
Residuals 83      7.41   0.089         0.690  0.198   
Total     95     10.74                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.6 Carbohydrate intake

7.1.9.6.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.234    2.53 0.044  0.574  
T1Dstatus              1      0.56   0.564    6.11 0.053  0.032 *
Carbs                  1      0.21   0.214    2.32 0.020  0.584  
seqRun                 3      0.68   0.228    2.46 0.064  0.667  
Tri                    2      0.11   0.055    0.60 0.010  0.638  
Age                    1      0.41   0.405    4.39 0.038  0.396  
Parity                 1      0.25   0.252    2.73 0.023  0.489  
BMI                    1      0.37   0.374    4.05 0.035  0.357  
Carb_Time_Interaction  1      0.09   0.091    0.99 0.008  0.672  
Residuals             82      7.57   0.092         0.705  0.266  
Total                 95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.6.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.234    2.52 0.044  0.614  
T1Dstatus              1      0.56   0.564    6.07 0.053  0.023 *
Carbs                  1      0.21   0.214    2.31 0.020  0.595  
seqRun                 3      0.68   0.228    2.45 0.064  0.686  
Tri                    2      0.11   0.055    0.59 0.010  0.601  
Age                    1      0.41   0.405    4.36 0.038  0.420  
Parity                 1      0.25   0.252    2.71 0.023  0.519  
BMI                    1      0.37   0.374    4.03 0.035  0.357  
Carb_Time_Interaction  1      0.04   0.043    0.46 0.004  0.992  
Residuals             82      7.62   0.093         0.710  0.379  
Total                 95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.6.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.234    2.52 0.044   0.59  
T1Dstatus              1      0.56   0.564    6.08 0.053   0.03 *
Carbs                  1      0.21   0.214    2.31 0.020   0.58  
seqRun                 3      0.68   0.228    2.45 0.064   0.66  
Tri                    2      0.11   0.055    0.59 0.010   0.62  
Age                    1      0.41   0.405    4.37 0.038   0.42  
Parity                 1      0.25   0.252    2.71 0.023   0.52  
BMI                    1      0.37   0.374    4.03 0.035   0.37  
Carb_Time_Interaction  1      0.05   0.051    0.55 0.005   0.91  
Residuals             82      7.61   0.093         0.709   0.31  
Total                 95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.6.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun     3      0.74   0.247    2.68 0.069  0.016 *
Tri        2      0.11   0.055    0.60 0.010  0.693  
Age        1      0.40   0.404    4.37 0.038  0.838  
Parity     1      0.27   0.270    2.92 0.025  0.042 *
BMI        1      0.35   0.354    3.83 0.033  0.931  
HLA        2      0.45   0.226    2.45 0.042  0.586  
T1Dstatus  1      0.48   0.478    5.18 0.045  0.055 .
Carbs      1      0.26   0.262    2.84 0.024  0.358  
Residuals 83      7.66   0.092         0.714  0.232  
Total     95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.7 Fibre intake

7.1.9.7.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.47   0.234    2.47 0.044  0.567  
T1Dstatus               1      0.56   0.564    5.97 0.053  0.024 *
Fiber                   1      0.13   0.127    1.34 0.012  0.923  
seqRun                  3      0.66   0.221    2.33 0.062  0.758  
Tri                     2      0.11   0.057    0.60 0.011  0.583  
Age                     1      0.41   0.413    4.36 0.038  0.394  
Parity                  1      0.25   0.247    2.61 0.023  0.584  
BMI                     1      0.34   0.336    3.55 0.031  0.559  
Fiber_Time_Interaction  1      0.05   0.053    0.56 0.005  0.766  
Residuals              82      7.75   0.095         0.722  0.454  
Total                  95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.7.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.47   0.234    2.47 0.044  0.585  
T1Dstatus               1      0.56   0.564    5.96 0.053  0.025 *
Fiber                   1      0.13   0.127    1.34 0.012  0.899  
seqRun                  3      0.66   0.221    2.33 0.062  0.755  
Tri                     2      0.11   0.057    0.60 0.011  0.633  
Age                     1      0.41   0.413    4.35 0.038  0.366  
Parity                  1      0.25   0.247    2.60 0.023  0.570  
BMI                     1      0.34   0.336    3.54 0.031  0.566  
Fiber_Time_Interaction  1      0.04   0.037    0.39 0.003  0.946  
Residuals              82      7.77   0.095         0.724  0.516  
Total                  95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.7.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.47   0.234    2.47 0.044  0.567  
T1Dstatus               1      0.56   0.564    5.96 0.053  0.028 *
Fiber                   1      0.13   0.127    1.34 0.012  0.907  
seqRun                  3      0.66   0.221    2.33 0.062  0.779  
Tri                     2      0.11   0.057    0.60 0.011  0.609  
Age                     1      0.41   0.413    4.36 0.038  0.352  
Parity                  1      0.25   0.247    2.61 0.023  0.570  
BMI                     1      0.34   0.336    3.55 0.031  0.570  
Fiber_Time_Interaction  1      0.05   0.048    0.51 0.004  0.701  
Residuals              82      7.76   0.095         0.723  0.443  
Total                  95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.7.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun     3      0.74   0.247    2.63 0.069  0.021 *
Tri        2      0.11   0.055    0.59 0.010  0.670  
Age        1      0.40   0.404    4.29 0.038  0.814  
Parity     1      0.27   0.270    2.87 0.025  0.036 *
BMI        1      0.35   0.354    3.76 0.033  0.920  
HLA        2      0.45   0.226    2.40 0.042  0.550  
T1Dstatus  1      0.48   0.478    5.08 0.045  0.060 .
Fiber      1      0.12   0.120    1.28 0.011  0.883  
Residuals 83      7.81   0.094         0.727  0.423  
Total     95     10.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.8 1,5-AG (glucose control measurement)

7.1.9.8.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.50   0.248    2.75 0.048  0.518  
T1Dstatus             1      0.63   0.632    7.00 0.062  0.015 *
Days                  1      0.12   0.117    1.29 0.011  0.197  
seqRun                3      0.62   0.208    2.31 0.061  0.865  
Age                   1      0.45   0.451    4.99 0.044  0.245  
Parity                1      0.24   0.238    2.64 0.023  0.665  
BMI                   1      0.26   0.260    2.88 0.025  0.850  
AG15                  1      0.29   0.289    3.21 0.028  0.015 *
AG15_T1D_Interaction  1      0.18   0.179    1.98 0.018  0.779  
Residuals            77      6.95   0.090         0.679  0.068 .
Total                89     10.24                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.8.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.29   0.146    2.39 0.072  0.778   
Days       1      0.27   0.268    4.39 0.066  0.009 **
seqRun     3      0.64   0.214    3.51 0.158  0.780   
Age        1      0.27   0.273    4.48 0.067  0.546   
Parity     1      0.38   0.380    6.23 0.094  0.007 **
BMI        1      0.24   0.244    4.01 0.060  0.844   
AG15       1      0.06   0.065    1.06 0.016  0.923   
Residuals 31      1.89   0.061         0.466  0.390   
Total     41      4.05                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.8.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.68   0.342    4.36 0.121  0.233  
Days       1      0.13   0.128    1.62 0.023  0.058 .
seqRun     3      0.59   0.198    2.52 0.105  0.875  
Age        1      0.78   0.776    9.89 0.138  0.067 .
Parity     1      0.13   0.135    1.72 0.024  0.952  
BMI        1      0.20   0.199    2.54 0.035  0.660  
AG15       1      0.22   0.225    2.86 0.040  0.771  
Residuals 37      2.90   0.079         0.515  0.296  
Total     47      5.64                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.2 Differential abundance analysis Genus taxonomic level

Controlling for multiple measurements, sequencing run, conception age, BMI, parity and HLA type

       nonT1D_vs_T1D  T1  T2  T3 T1_vs_T2 T2_vs_T3 T1_vs_T3 T1DT1vsT2 T1DT2vsT3 T1DT1vsT3
Down               0   0   0   0        0        0        0         0         0         0
NotSig           113 113 113 113      113      113      113       113       113       113
Up                 0   0   0   0        0        0        0         0         0         0
       noT1DT1vsT2 noT1DT2vsT3 noT1DT1vsT3
Down             0           0           0
NotSig         113         113         113
Up               0           0           0

No differentially abundant (i.e. all adjusted P-values > 0.1) genera were detected between T1D and non-T1D women accross trimesters or in each trimesters separatelly (i.e. nonT1D_vs_T1D, T1, T2 and T3 contrasts had no strains up or down). In addition no differences between trimesters were detected in samples from T1D and non-T1D women together or separatelly.

Results for contrasts with significant differentially abundant strains shown below

7.2.1 Across all trimesters (T1D vs non-T1D)

[1] "No DA taxa found"

7.2.2 Only Trimester 1 (nonT1D vs T1D)

[1] "No DA taxa found"

7.2.3 Only Trimester 2 (nonT1D vs T1D)

[1] "No DA taxa found"

7.2.4 Only Trimester 3 (nonT1D vs T1D)

[1] "No DA taxa found"

7.2.5 T1 vs T2 (All data)

[1] "No DA taxa found"

7.2.6 T2 vs T3 (All data)

[1] "No DA taxa"

7.2.7 T1 vs T3 (All data)

[1] "No DA taxa found"

7.2.8 T1 vs T2 (in women with T1D)

[1] "No DA taxa found"

7.2.9 T2 vs T3 (in women with T1D)

[1] "No DA taxa found"

7.2.10 T1 vs T3 (in women with T1D)

[1] "No DA taxa found"

7.2.11 T1 vs T2 (in women without T1D)

[1] "No DA taxa found"

7.2.12 T2 vs T3 (in women without T1D)

[1] "No DA taxa found"

7.2.13 T1 vs T3 (in women without T1D)

[1] "No DA taxa found"

8 Family taxonomic level

8.1 Microbial community composition analysis at Family level (Beta diversity analysis)

8.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun                3      0.58   0.195    2.61 0.068  0.001 ***
Days                  1      0.10   0.102    1.37 0.012  0.079 .  
T1D_Time_Interaction  1      0.48   0.482    6.46 0.056  0.007 ** 
Age                   1      0.29   0.292    3.91 0.034  0.990    
Parity                1      0.18   0.177    2.38 0.021  0.006 ** 
BMI                   1      0.17   0.167    2.24 0.020  0.989    
HLA                   2      0.41   0.204    2.73 0.048  0.339    
T1Dstatus             1      0.07   0.067    0.90 0.008  0.943    
Residuals            84      6.27   0.075         0.733  0.360    
Total                95      8.55                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.007

8.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3     0.267  0.0889   0.911 0.120   0.55
Nulliparous     1     0.174  0.1740   1.782 0.078   0.11
Age_LMP         1     0.128  0.1276   1.307 0.058   0.26
BMI_conception  1     0.081  0.0814   0.834 0.037   0.58
HLA.6DRML       2     0.174  0.0870   0.891 0.078   0.55
T1Dstatus       1     0.127  0.1265   1.296 0.057   0.26
Residuals      13     1.269  0.0976         0.572       
Total          22     2.219                 1.000       
[1] 0.264

Beta diversity Plot

8.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3     0.343  0.1144   1.287 0.119   0.20
Nulliparous     1     0.077  0.0765   0.861 0.027   0.53
Age_LMP         1     0.116  0.1164   1.310 0.040   0.26
BMI_conception  1     0.114  0.1143   1.286 0.040   0.24
HLA.6DRML       2     0.173  0.0866   0.974 0.060   0.44
T1Dstatus       1     0.103  0.1033   1.162 0.036   0.32
Residuals      22     1.956  0.0889         0.678       
Total          31     2.882                 1.000       
[1] 0.32

Beta diversity Plot

8.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
SeqRun          3     0.167  0.0557    0.68 0.060  0.848   
Nulliparous     1     0.104  0.1042    1.26 0.037  0.239   
Age_LMP         1     0.108  0.1077    1.30 0.039  0.257   
BMI_conception  1     0.187  0.1872    2.27 0.067  0.048 * 
HLA.6DRML       2     0.120  0.0601    0.73 0.043  0.725   
T1Dstatus       1     0.276  0.2756    3.34 0.099  0.006 **
Residuals      22     1.816  0.0826         0.654          
Total          31     2.778                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.006

Beta diversity Plot

8.1.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.28  0.1400    3.05 0.080  0.530   
seqRun     3      0.71  0.2360    5.14 0.203  0.476   
Age        1      0.21  0.2128    4.63 0.061  0.504   
Parity     1      0.28  0.2798    6.09 0.080  0.010 **
BMI        1      0.18  0.1771    3.85 0.051  0.818   
Days       1      0.09  0.0905    1.97 0.026  0.051 . 
Residuals 38      1.75  0.0459         0.500  0.038 * 
Total     47      3.49                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

8.1.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.28  0.1400    3.01 0.080  0.550   
seqRun     3      0.71  0.2360    5.08 0.203  0.484   
Age        1      0.21  0.2128    4.58 0.061  0.466   
Parity     1      0.28  0.2798    6.02 0.080  0.010 **
BMI        1      0.18  0.1771    3.81 0.051  0.829   
Tri        2      0.12  0.0583    1.25 0.033  0.128   
Residuals 37      1.72  0.0465         0.492  0.069 . 
Total     47      3.49                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

8.1.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.53   0.263    3.65 0.112  0.288  
seqRun     3      0.38   0.127    1.76 0.081  0.946  
Age        1      0.62   0.617    8.56 0.132  0.116  
Parity     1      0.11   0.108    1.50 0.023  0.907  
BMI        1      0.18   0.176    2.45 0.038  0.286  
Days       1      0.13   0.131    1.82 0.028  0.025 *
Residuals 38      2.74   0.072         0.586  0.282  
Total     47      4.68                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

8.1.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2      0.53   0.263    3.56 0.112   0.29
seqRun     3      0.38   0.127    1.71 0.081   0.93
Age        1      0.62   0.617    8.35 0.132   0.12
Parity     1      0.11   0.108    1.47 0.023   0.92
BMI        1      0.18   0.176    2.39 0.038   0.28
Tri        2      0.14   0.068    0.92 0.029   0.26
Residuals 37      2.74   0.074         0.585   0.31
Total     47      4.68                 1.000       

Beta diversity Plot

8.1.9 Other factors

8.1.9.1 Age at conception

8.1.9.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.36   0.179    2.33 0.042  0.564  
T1Dstatus             1      0.41   0.408    5.30 0.048  0.056 .
seqRun                3      0.61   0.203    2.64 0.071  0.342  
Tri                   2      0.09   0.046    0.59 0.011  0.587  
Age                   1      0.30   0.299    3.88 0.035  0.341  
Parity                1      0.17   0.167    2.17 0.020  0.611  
BMI                   1      0.19   0.193    2.51 0.023  0.802  
Age_Time_Interaction  1      0.03   0.033    0.43 0.004  0.747  
Residuals            83      6.39   0.077         0.747  0.248  
Total                95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.36   0.179    2.32 0.042  0.549  
T1Dstatus             1      0.41   0.408    5.28 0.048  0.064 .
seqRun                3      0.61   0.203    2.63 0.071  0.339  
Tri                   2      0.09   0.046    0.59 0.011  0.571  
Age                   1      0.30   0.299    3.86 0.035  0.326  
Parity                1      0.17   0.167    2.17 0.020  0.629  
BMI                   1      0.19   0.193    2.50 0.023  0.799  
Age_Time_Interaction  1      0.01   0.010    0.13 0.001  0.982  
Residuals            83      6.41   0.077         0.750  0.309  
Total                95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.36   0.179    2.33 0.042  0.545  
T1Dstatus             1      0.41   0.408    5.30 0.048  0.062 .
seqRun                3      0.61   0.203    2.64 0.071  0.338  
Tri                   2      0.09   0.046    0.59 0.011  0.572  
Age                   1      0.30   0.299    3.88 0.035  0.326  
Parity                1      0.17   0.167    2.17 0.020  0.623  
BMI                   1      0.19   0.193    2.51 0.023  0.801  
Age_Time_Interaction  1      0.04   0.035    0.46 0.004  0.639  
Residuals            83      6.39   0.077         0.747  0.236  
Total                95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.1.4 Age at conception (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.36   0.179    2.35 0.042   0.53  
T1Dstatus  1      0.41   0.408    5.34 0.048   0.05 *
seqRun     3      0.61   0.203    2.65 0.071   0.33  
Tri        2      0.09   0.046    0.60 0.011   0.54  
Parity     1      0.15   0.145    1.90 0.017   0.72  
BMI        1      0.25   0.248    3.25 0.029   0.68  
Age        1      0.27   0.265    3.47 0.031   0.47  
Residuals 84      6.42   0.076         0.751   0.20  
Total     95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.2 Body max index (BMI)

8.1.9.2.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.36   0.179    2.32 0.042  0.555  
T1Dstatus             1      0.41   0.408    5.28 0.048  0.057 .
seqRun                3      0.61   0.203    2.63 0.071  0.358  
Tri                   2      0.09   0.046    0.59 0.011  0.567  
Age                   1      0.30   0.299    3.87 0.035  0.295  
Parity                1      0.17   0.167    2.17 0.020  0.627  
BMI                   1      0.19   0.193    2.50 0.023  0.797  
BMI_Time_Interaction  1      0.01   0.011    0.14 0.001  0.957  
Residuals            83      6.41   0.077         0.750  0.279  
Total                95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.2.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.36   0.179    2.32 0.042  0.563  
T1Dstatus             1      0.41   0.408    5.29 0.048  0.055 .
seqRun                3      0.61   0.203    2.63 0.071  0.328  
Tri                   2      0.09   0.046    0.59 0.011  0.545  
Age                   1      0.30   0.299    3.87 0.035  0.308  
Parity                1      0.17   0.167    2.17 0.020  0.655  
BMI                   1      0.19   0.193    2.50 0.023  0.810  
BMI_Time_Interaction  1      0.01   0.013    0.17 0.001  0.932  
Residuals            83      6.41   0.077         0.750  0.246  
Total                95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.2.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.36   0.179    2.33 0.042   0.53  
T1Dstatus             1      0.41   0.408    5.31 0.048   0.06 .
seqRun                3      0.61   0.203    2.64 0.071   0.35  
Tri                   2      0.09   0.046    0.59 0.011   0.54  
Age                   1      0.30   0.299    3.88 0.035   0.34  
Parity                1      0.17   0.167    2.18 0.020   0.61  
BMI                   1      0.19   0.193    2.51 0.023   0.81  
BMI_Time_Interaction  1      0.04   0.040    0.53 0.005   0.34  
Residuals            83      6.38   0.077         0.747   0.18  
Total                95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.2.4 BMI (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.36   0.179    2.35 0.042  0.582  
T1Dstatus  1      0.41   0.408    5.34 0.048  0.064 .
seqRun     3      0.61   0.203    2.65 0.071  0.359  
Tri        2      0.09   0.046    0.60 0.011  0.542  
Age        1      0.30   0.299    3.90 0.035  0.338  
Parity     1      0.17   0.167    2.19 0.020  0.630  
BMI        1      0.19   0.193    2.53 0.023  0.775  
Residuals 84      6.42   0.076         0.751  0.234  
Total     95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.3 HLA type

8.1.9.3.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.36   0.179    2.35 0.042  0.556  
T1Dstatus             1      0.41   0.408    5.35 0.048  0.061 .
Days                  1      0.11   0.110    1.44 0.013  0.075 .
seqRun                3      0.60   0.199    2.61 0.070  0.374  
Age                   1      0.29   0.286    3.75 0.034  0.368  
Parity                1      0.16   0.164    2.15 0.019  0.700  
BMI                   1      0.19   0.188    2.46 0.022  0.818  
HLA_Time_Interaction  1      0.03   0.026    0.35 0.003  1.000  
Residuals            84      6.41   0.076         0.750  0.487  
Total                95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.3.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.36   0.179    2.36 0.042  0.570  
T1Dstatus             1      0.41   0.408    5.38 0.048  0.064 .
Days                  1      0.11   0.110    1.45 0.013  0.074 .
seqRun                3      0.60   0.199    2.62 0.070  0.369  
Age                   1      0.29   0.286    3.77 0.034  0.402  
Parity                1      0.16   0.164    2.16 0.019  0.708  
BMI                   1      0.19   0.188    2.47 0.022  0.816  
HLA_Time_Interaction  1      0.06   0.059    0.78 0.007  0.998  
Residuals            84      6.38   0.076         0.746  0.336  
Total                95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.3.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.36   0.179    2.36 0.042  0.553  
T1Dstatus             1      0.41   0.408    5.36 0.048  0.064 .
Days                  1      0.11   0.110    1.44 0.013  0.064 .
seqRun                3      0.60   0.199    2.62 0.070  0.383  
Age                   1      0.29   0.286    3.76 0.034  0.388  
Parity                1      0.16   0.164    2.15 0.019  0.677  
BMI                   1      0.19   0.188    2.47 0.022  0.838  
HLA_Time_Interaction  1      0.04   0.039    0.51 0.005  0.829  
Residuals            84      6.40   0.076         0.748  0.207  
Total                95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.3.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days       1      0.12   0.115    1.52 0.013  0.059 . 
seqRun     3      0.57   0.190    2.51 0.067  0.852   
Age        1      0.27   0.267    3.53 0.031  0.998   
Parity     1      0.19   0.187    2.47 0.022  0.002 **
BMI        1      0.24   0.236    3.12 0.028  0.901   
T1Dstatus  1      0.35   0.352    4.65 0.041  0.090 . 
HLA        2      0.38   0.192    2.54 0.045  0.461   
Residuals 85      6.43   0.076         0.753  0.168   
Total     95      8.55                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.4 Parity

8.1.9.4.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.36   0.179    2.37 0.042  0.543  
T1Dstatus                1      0.41   0.408    5.39 0.048  0.062 .
Days                     1      0.11   0.110    1.45 0.013  0.071 .
seqRun                   3      0.60   0.199    2.63 0.070  0.393  
Age                      1      0.29   0.286    3.79 0.034  0.393  
Parity                   1      0.16   0.164    2.17 0.019  0.688  
BMI                      1      0.19   0.188    2.48 0.022  0.833  
Parity_Time_Interaction  1      0.08   0.079    1.04 0.009  0.134  
Residuals               84      6.36   0.076         0.744  0.138  
Total                   95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.4.2 Parity (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.36   0.179    2.37 0.042  0.550  
T1Dstatus  1      0.41   0.408    5.39 0.048  0.066 .
Days       1      0.11   0.110    1.45 0.013  0.069 .
seqRun     3      0.60   0.199    2.63 0.070  0.374  
BMI        1      0.31   0.306    4.04 0.036  0.481  
Age        1      0.25   0.248    3.27 0.029  0.450  
Parity     1      0.09   0.085    1.12 0.010  0.951  
Residuals 85      6.43   0.076         0.753  0.174  
Total     95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.5 Mode of delivery

8.1.9.5.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                   2      0.36   0.179    2.51 0.042  0.544   
T1Dstatus             1      0.41   0.408    5.70 0.048  0.064 . 
MOD                   2      0.31   0.155    2.16 0.036  0.675   
Days                  1      0.11   0.111    1.55 0.013  0.054 . 
seqRun                3      0.59   0.198    2.77 0.069  0.378   
Age                   1      0.49   0.486    6.79 0.057  0.005 **
Parity                1      0.15   0.150    2.09 0.017  0.781   
BMI                   1      0.20   0.202    2.82 0.024  0.675   
MOD_Time_Interaction  1      0.06   0.061    0.86 0.007  0.990   
Residuals            82      5.87   0.072         0.686  0.180   
Total                95      8.55                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.5.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                   2      0.36   0.179    2.50 0.042  0.565   
T1Dstatus             1      0.41   0.408    5.69 0.048  0.057 . 
MOD                   2      0.31   0.155    2.16 0.036  0.686   
Days                  1      0.11   0.111    1.54 0.013  0.062 . 
seqRun                3      0.59   0.198    2.76 0.069  0.409   
Age                   1      0.49   0.486    6.78 0.057  0.004 **
Parity                1      0.15   0.150    2.09 0.017  0.752   
BMI                   1      0.20   0.202    2.81 0.024  0.666   
MOD_Time_Interaction  1      0.05   0.051    0.71 0.006  1.000   
Residuals            82      5.88   0.072         0.688  0.302   
Total                95      8.55                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.5.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                   2      0.36   0.179    2.50 0.042  0.575   
T1Dstatus             1      0.41   0.408    5.70 0.048  0.068 . 
MOD                   2      0.31   0.155    2.16 0.036  0.685   
Days                  1      0.11   0.111    1.54 0.013  0.050 * 
seqRun                3      0.59   0.198    2.76 0.069  0.383   
Age                   1      0.49   0.486    6.78 0.057  0.005 **
Parity                1      0.15   0.150    2.09 0.017  0.763   
BMI                   1      0.20   0.202    2.81 0.024  0.667   
MOD_Time_Interaction  1      0.05   0.053    0.74 0.006  0.999   
Residuals            82      5.88   0.072         0.687  0.390   
Total                95      8.55                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.5.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days       1      0.12   0.115    1.61 0.013  0.069 . 
seqRun     3      0.57   0.190    2.67 0.067  0.827   
Age        1      0.27   0.267    3.74 0.031  0.994   
Parity     1      0.19   0.187    2.62 0.022  0.002 **
BMI        1      0.24   0.236    3.30 0.028  0.885   
HLA        2      0.34   0.172    2.41 0.040  0.532   
T1Dstatus  1      0.39   0.391    5.48 0.046  0.070 . 
MOD        2      0.51   0.253    3.54 0.059  0.223   
Residuals 83      5.93   0.071         0.694  0.117   
Total     95      8.55                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.6 Carbohydrate intake

8.1.9.6.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.36   0.179    2.44 0.042   0.57  
T1Dstatus              1      0.41   0.408    5.54 0.048   0.06 .
Carbs                  1      0.25   0.246    3.35 0.029   0.26  
seqRun                 3      0.61   0.204    2.77 0.072   0.34  
Tri                    2      0.09   0.043    0.59 0.010   0.59  
Age                    1      0.28   0.276    3.75 0.032   0.47  
Parity                 1      0.18   0.184    2.49 0.021   0.37  
BMI                    1      0.26   0.264    3.59 0.031   0.30  
Carb_Time_Interaction  1      0.07   0.073    1.00 0.009   0.77  
Residuals             82      6.04   0.074         0.706   0.16  
Total                 95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.6.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.36   0.179    2.43 0.042  0.523  
T1Dstatus              1      0.41   0.408    5.52 0.048  0.065 .
Carbs                  1      0.25   0.246    3.33 0.029  0.266  
seqRun                 3      0.61   0.204    2.76 0.072  0.371  
Tri                    2      0.09   0.043    0.59 0.010  0.598  
Age                    1      0.28   0.276    3.73 0.032  0.464  
Parity                 1      0.18   0.184    2.48 0.021  0.370  
BMI                    1      0.26   0.264    3.57 0.031  0.292  
Carb_Time_Interaction  1      0.04   0.044    0.59 0.005  0.972  
Residuals             82      6.07   0.074         0.710  0.214  
Total                 95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.6.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.36   0.179    2.43 0.042  0.541  
T1Dstatus              1      0.41   0.408    5.52 0.048  0.042 *
Carbs                  1      0.25   0.246    3.33 0.029  0.294  
seqRun                 3      0.61   0.204    2.76 0.072  0.344  
Tri                    2      0.09   0.043    0.59 0.010  0.592  
Age                    1      0.28   0.276    3.74 0.032  0.450  
Parity                 1      0.18   0.184    2.48 0.021  0.387  
BMI                    1      0.26   0.264    3.57 0.031  0.319  
Carb_Time_Interaction  1      0.05   0.048    0.64 0.006  0.894  
Residuals             82      6.06   0.074         0.709  0.172  
Total                 95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.6.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3      0.58   0.195    2.64 0.068  0.001 ***
Tri        2      0.08   0.042    0.58 0.010  0.637    
Age        1      0.28   0.279    3.79 0.033  0.850    
Parity     1      0.19   0.186    2.53 0.022  0.021 *  
BMI        1      0.24   0.235    3.20 0.028  0.901    
HLA        2      0.35   0.173    2.35 0.041  0.566    
T1Dstatus  1      0.41   0.410    5.57 0.048  0.043 *  
Carbs      1      0.31   0.310    4.21 0.036  0.140    
Residuals 83      6.11   0.074         0.715  0.120    
Total     95      8.55                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.7 Fibre intake

8.1.9.7.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.36   0.179    2.35 0.042  0.573  
T1Dstatus               1      0.41   0.408    5.33 0.048  0.048 *
Fiber                   1      0.13   0.132    1.72 0.015  0.711  
seqRun                  3      0.59   0.197    2.58 0.069  0.418  
Tri                     2      0.09   0.046    0.60 0.011  0.542  
Age                     1      0.27   0.269    3.52 0.031  0.493  
Parity                  1      0.17   0.175    2.29 0.020  0.506  
BMI                     1      0.22   0.220    2.88 0.026  0.588  
Fiber_Time_Interaction  1      0.03   0.027    0.35 0.003  0.929  
Residuals              82      6.27   0.077         0.734  0.436  
Total                  95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.7.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.36   0.179    2.35 0.042  0.551  
T1Dstatus               1      0.41   0.408    5.34 0.048  0.043 *
Fiber                   1      0.13   0.132    1.72 0.015  0.716  
seqRun                  3      0.59   0.197    2.58 0.069  0.411  
Tri                     2      0.09   0.046    0.60 0.011  0.515  
Age                     1      0.27   0.269    3.52 0.031  0.512  
Parity                  1      0.17   0.175    2.29 0.020  0.489  
BMI                     1      0.22   0.220    2.88 0.026  0.595  
Fiber_Time_Interaction  1      0.03   0.034    0.44 0.004  0.876  
Residuals              82      6.27   0.076         0.733  0.416  
Total                  95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.7.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.36   0.179    2.35 0.042  0.596  
T1Dstatus               1      0.41   0.408    5.35 0.048  0.052 .
Fiber                   1      0.13   0.132    1.72 0.015  0.704  
seqRun                  3      0.59   0.197    2.58 0.069  0.401  
Tri                     2      0.09   0.046    0.60 0.011  0.538  
Age                     1      0.27   0.269    3.53 0.031  0.470  
Parity                  1      0.17   0.175    2.29 0.020  0.491  
BMI                     1      0.22   0.220    2.88 0.026  0.586  
Fiber_Time_Interaction  1      0.04   0.040    0.53 0.005  0.708  
Residuals              82      6.26   0.076         0.732  0.395  
Total                  95      8.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.7.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3      0.58   0.195    2.57 0.068  0.001 ***
Tri        2      0.08   0.042    0.56 0.010  0.626    
Age        1      0.28   0.279    3.67 0.033  0.848    
Parity     1      0.19   0.186    2.45 0.022  0.018 *  
BMI        1      0.24   0.235    3.10 0.028  0.916    
HLA        2      0.35   0.173    2.28 0.041  0.555    
T1Dstatus  1      0.41   0.410    5.40 0.048  0.048 *  
Fiber      1      0.12   0.121    1.59 0.014  0.733    
Residuals 83      6.30   0.076         0.737  0.341    
Total     95      8.55                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.8 1,5-AG (glucose control measurement)

8.1.9.8.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.38   0.189    2.53 0.046  0.532  
T1Dstatus             1      0.49   0.491    6.59 0.060  0.027 *
Days                  1      0.11   0.113    1.51 0.014  0.112  
seqRun                3      0.53   0.177    2.37 0.065  0.675  
Age                   1      0.32   0.316    4.23 0.038  0.272  
Parity                1      0.17   0.174    2.33 0.021  0.570  
BMI                   1      0.15   0.150    2.01 0.018  0.895  
AG15                  1      0.22   0.225    3.02 0.027  0.028 *
AG15_T1D_Interaction  1      0.10   0.101    1.35 0.012  0.954  
Residuals            77      5.74   0.075         0.699  0.107  
Total                89      8.21                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.8.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2     0.245  0.1226    2.66 0.080  0.606   
Days       1     0.221  0.2209    4.80 0.072  0.015 * 
seqRun     3     0.591  0.1969    4.28 0.192  0.702   
Age        1     0.121  0.1211    2.63 0.039  0.680   
Parity     1     0.302  0.3017    6.56 0.098  0.003 **
BMI        1     0.138  0.1377    2.99 0.045  0.894   
AG15       1     0.031  0.0307    0.67 0.010  0.980   
Residuals 31     1.427  0.0460         0.464  0.216   
Total     41     3.075                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.8.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.53   0.263    3.79 0.112  0.283  
Days       1      0.14   0.137    1.97 0.029  0.031 *
seqRun     3      0.39   0.129    1.85 0.083  0.910  
Age        1      0.61   0.610    8.78 0.130  0.116  
Parity     1      0.11   0.115    1.65 0.025  0.891  
BMI        1      0.16   0.165    2.37 0.035  0.368  
AG15       1      0.17   0.170    2.45 0.036  0.807  
Residuals 37      2.57   0.070         0.549  0.408  
Total     47      4.68                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.2 Differential abundance analysis Family taxonomic level

Controlling for multiple measurements, sequencing run, conception age, BMI, parity and HLA type

       nonT1D_vs_T1D T1 T2 T3 T1_vs_T2 T2_vs_T3 T1_vs_T3 T1DT1vsT2 T1DT2vsT3 T1DT1vsT3
Down               0  0  0  0        0        0        0         0         0         0
NotSig            52 52 52 52       52       52       51        52        52        52
Up                 0  0  0  0        0        0        1         0         0         0
       noT1DT1vsT2 noT1DT2vsT3 noT1DT1vsT3
Down             0           0           0
NotSig          52          22          52
Up               0          30           0

Results for contrasts with significant (or borderline significant) differences shown below

8.2.1 Across all trimesters (T1D vs non-T1D)

      Classification  LogFC   P.Val adj.P.Val nonT1D:mean% Prev% T1D:mean% T1D:Prev%
2 Enterobacteriaceae -0.897 0.00342    0.0890        0.146  97.9     1.186     100.0
1     Prevotellaceae  1.253 0.00097    0.0504        5.199 100.0     0.957      97.9
[1] 30

8.2.2 Only Trimester 1 (nonT1D vs T1D)

[1] "No DA taxa found"

8.2.3 Only Trimester 2 (nonT1D vs T1D)

  Classification LogFC   P.Val adj.P.Val mean% Prev%
1 Prevotellaceae  1.39 0.00124    0.0647  5.25 100.0
2 Prevotellaceae  1.39 0.00124    0.0647  1.28  93.8

8.2.4 Only Trimester 3 (nonT1D vs T1D)

  Classification LogFC  P.Val adj.P.Val mean% Prev%
1 Bacteroidaceae -1.32 0.0015    0.0778  18.8   100
2 Bacteroidaceae -1.32 0.0015    0.0778  34.1   100
[1] 31

8.2.5 T1 vs T2 (All data)

[1] "No DA taxa found"

8.2.6 T2 vs T3 (All data)

[1] "No DA taxa"

8.2.7 T1 vs T3 (All data)

[1] Classification LogFC          P.Val          adj.P.Val      mean%         
[6] Prev%         
<0 rows> (or 0-length row.names)

8.2.8 T1 vs T2 (in women with T1D)

[1] "No DA taxa found"

8.2.9 T2 vs T3 (in women with T1D)

[1] "No DA taxa found"

8.2.10 T1 vs T3 (in women with T1D)

[1] "No DA taxa found"

8.2.11 T1 vs T2 (in women without T1D)

[1] "No DA taxa found"

8.2.12 T2 vs T3 (in women without T1D)

   Classification LogFC    P.Val adj.P.Val T2:mean% T2Prev% T3:mean% T3Prev%
1 Pasteurellaceae 0.549 0.000819    0.0391    0.177      70    0.052    52.9
[1] 15

8.2.13 T1 vs T3 (in women without T1D)

[1] "No DA taxa found"

9 Order taxonomic level

9.1 Microbial community composition analysis at Order level (Beta diversity analysis)

9.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun                3      0.39   0.131    3.44 0.094  0.001 ***
Days                  1      0.01   0.007    0.18 0.002  0.829    
T1D_Time_Interaction  1      0.33   0.331    8.71 0.079  0.023 *  
Age                   1      0.05   0.049    1.29 0.012  0.402    
Parity                1      0.06   0.055    1.46 0.013  0.514    
BMI                   1      0.06   0.058    1.54 0.014  0.836    
HLA                   2      0.07   0.033    0.86 0.016  0.820    
T1Dstatus             1      0.03   0.029    0.77 0.007  0.713    
Residuals            84      3.19   0.038         0.764  0.668    
Total                95      4.18                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.023

9.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
SeqRun          3     0.129  0.0430    1.10 0.124  0.356   
Nulliparous     1     0.241  0.2415    6.20 0.232  0.009 **
Age_LMP         1     0.020  0.0199    0.51 0.019  0.565   
BMI_conception  1     0.010  0.0098    0.25 0.009  0.845   
HLA.6DRML       2     0.058  0.0290    0.74 0.056  0.533   
T1Dstatus       1     0.076  0.0764    1.96 0.073  0.156   
Residuals      13     0.507  0.0390         0.487          
Total          22     1.041                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.156

Beta diversity Plot

9.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3     0.185  0.0618   1.287 0.130   0.29
Nulliparous     1     0.016  0.0162   0.337 0.011   0.69
Age_LMP         1     0.020  0.0197   0.411 0.014   0.64
BMI_conception  1     0.072  0.0719   1.498 0.051   0.21
HLA.6DRML       2     0.010  0.0051   0.107 0.007   0.99
T1Dstatus       1     0.062  0.0622   1.296 0.044   0.24
Residuals      22     1.057  0.0480         0.743       
Total          31     1.422                 1.000       
[1] 0.239

Beta diversity Plot

9.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3     0.099  0.0331    0.88 0.077  0.497  
Nulliparous     1     0.031  0.0313    0.83 0.024  0.410  
Age_LMP         1     0.033  0.0329    0.87 0.026  0.377  
BMI_conception  1     0.120  0.1195    3.18 0.093  0.061 .
HLA.6DRML       2     0.018  0.0092    0.24 0.014  0.950  
T1Dstatus       1     0.157  0.1574    4.19 0.122  0.032 *
Residuals      22     0.827  0.0376         0.643         
Total          31     1.286                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.032

Beta diversity Plot

9.1.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.063  0.0315    1.48 0.048   0.69
seqRun     3     0.269  0.0896    4.20 0.205   0.45
Age        1     0.065  0.0655    3.07 0.050   0.67
Parity     1     0.044  0.0443    2.08 0.034   0.22
BMI        1     0.030  0.0296    1.39 0.023   0.62
Days       1     0.030  0.0297    1.39 0.023   0.20
Residuals 38     0.811  0.0214         0.618   0.64
Total     47     1.312                 1.000       

Beta diversity Plot

9.1.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.063  0.0315    1.49 0.048   0.70
seqRun     3     0.269  0.0896    4.24 0.205   0.46
Age        1     0.065  0.0655    3.10 0.050   0.68
Parity     1     0.044  0.0443    2.10 0.034   0.23
BMI        1     0.030  0.0296    1.40 0.023   0.60
Tri        2     0.059  0.0293    1.38 0.045   0.18
Residuals 37     0.782  0.0211         0.596   0.53
Total     47     1.312                 1.000       

Beta diversity Plot

9.1.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.285   0.143    3.21 0.112  0.336  
seqRun     3     0.147   0.049    1.10 0.058  0.955  
Age        1     0.318   0.318    7.15 0.125  0.068 .
Parity     1     0.028   0.028    0.63 0.011  0.945  
BMI        1     0.018   0.018    0.40 0.007  0.889  
Days       1     0.061   0.061    1.36 0.024  0.153  
Residuals 38     1.691   0.045         0.664  0.523  
Total     47     2.548                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

9.1.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.285   0.143    3.10 0.112  0.333  
seqRun     3     0.147   0.049    1.07 0.058  0.968  
Age        1     0.318   0.318    6.91 0.125  0.087 .
Parity     1     0.028   0.028    0.61 0.011  0.917  
BMI        1     0.018   0.018    0.39 0.007  0.885  
Tri        2     0.049   0.024    0.53 0.019  0.525  
Residuals 37     1.703   0.046         0.668  0.615  
Total     47     2.548                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

9.1.9 Other factors

9.1.9.1 Age at conception

9.1.9.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.96 0.018  0.826  
T1Dstatus             1      0.31  0.3066    7.89 0.073  0.068 .
seqRun                3      0.34  0.1123    2.89 0.081  0.622  
Tri                   2      0.04  0.0194    0.50 0.009  0.582  
Age                   1      0.05  0.0453    1.17 0.011  0.358  
Parity                1      0.06  0.0611    1.57 0.015  0.259  
BMI                   1      0.05  0.0534    1.37 0.013  0.853  
Age_Time_Interaction  1      0.04  0.0354    0.91 0.008  0.274  
Residuals            83      3.22  0.0388         0.772  0.426  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.95 0.018  0.817  
T1Dstatus             1      0.31  0.3066    7.82 0.073  0.038 *
seqRun                3      0.34  0.1123    2.86 0.081  0.623  
Tri                   2      0.04  0.0194    0.49 0.009  0.606  
Age                   1      0.05  0.0453    1.16 0.011  0.320  
Parity                1      0.06  0.0611    1.56 0.015  0.255  
BMI                   1      0.05  0.0534    1.36 0.013  0.876  
Age_Time_Interaction  1      0.00  0.0032    0.08 0.001  0.894  
Residuals            83      3.26  0.0392         0.780  0.502  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.97 0.018  0.790  
T1Dstatus             1      0.31  0.3066    7.94 0.073  0.044 *
seqRun                3      0.34  0.1123    2.91 0.081  0.643  
Tri                   2      0.04  0.0194    0.50 0.009  0.586  
Age                   1      0.05  0.0453    1.17 0.011  0.329  
Parity                1      0.06  0.0611    1.58 0.015  0.278  
BMI                   1      0.05  0.0534    1.38 0.013  0.873  
Age_Time_Interaction  1      0.05  0.0549    1.42 0.013  0.169  
Residuals            83      3.21  0.0386         0.767  0.401  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.1.4 Age at conception (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.07  0.0373    0.96 0.018  0.826  
T1Dstatus  1      0.31  0.3066    7.90 0.073  0.056 .
seqRun     3      0.34  0.1123    2.89 0.081  0.608  
Tri        2      0.04  0.0194    0.50 0.009  0.596  
Parity     1      0.06  0.0636    1.64 0.015  0.215  
BMI        1      0.05  0.0477    1.23 0.011  0.887  
Age        1      0.05  0.0486    1.25 0.012  0.492  
Residuals 84      3.26  0.0388         0.780  0.431  
Total     95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.2 Body max index (BMI)

9.1.9.2.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.96 0.018  0.824  
T1Dstatus             1      0.31  0.3066    7.85 0.073  0.045 *
seqRun                3      0.34  0.1123    2.87 0.081  0.628  
Tri                   2      0.04  0.0194    0.50 0.009  0.582  
Age                   1      0.05  0.0453    1.16 0.011  0.335  
Parity                1      0.06  0.0611    1.57 0.015  0.266  
BMI                   1      0.05  0.0534    1.37 0.013  0.859  
BMI_Time_Interaction  1      0.02  0.0191    0.49 0.005  0.473  
Residuals            83      3.24  0.0390         0.776  0.482  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.2.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.95 0.018  0.818  
T1Dstatus             1      0.31  0.3066    7.81 0.073  0.059 .
seqRun                3      0.34  0.1123    2.86 0.081  0.635  
Tri                   2      0.04  0.0194    0.49 0.009  0.617  
Age                   1      0.05  0.0453    1.16 0.011  0.323  
Parity                1      0.06  0.0611    1.56 0.015  0.288  
BMI                   1      0.05  0.0534    1.36 0.013  0.882  
BMI_Time_Interaction  1      0.00  0.0028    0.07 0.001  0.882  
Residuals            83      3.26  0.0392         0.780  0.503  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.2.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.96 0.018   0.82  
T1Dstatus             1      0.31  0.3066    7.86 0.073   0.06 .
seqRun                3      0.34  0.1123    2.88 0.081   0.61  
Tri                   2      0.04  0.0194    0.50 0.009   0.60  
Age                   1      0.05  0.0453    1.16 0.011   0.32  
Parity                1      0.06  0.0611    1.57 0.015   0.27  
BMI                   1      0.05  0.0534    1.37 0.013   0.86  
BMI_Time_Interaction  1      0.02  0.0203    0.52 0.005   0.34  
Residuals            83      3.24  0.0390         0.776   0.45  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.2.4 BMI (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.07  0.0373    0.96 0.018  0.817  
T1Dstatus  1      0.31  0.3066    7.90 0.073  0.057 .
seqRun     3      0.34  0.1123    2.89 0.081  0.643  
Tri        2      0.04  0.0194    0.50 0.009  0.591  
Age        1      0.05  0.0453    1.17 0.011  0.311  
Parity     1      0.06  0.0611    1.58 0.015  0.256  
BMI        1      0.05  0.0534    1.38 0.013  0.876  
Residuals 84      3.26  0.0388         0.780  0.435  
Total     95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.3 HLA type

9.1.9.3.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.96 0.018  0.807  
T1Dstatus             1      0.31  0.3066    7.85 0.073  0.059 .
Days                  1      0.01  0.0066    0.17 0.002  0.848  
seqRun                3      0.33  0.1114    2.85 0.080  0.643  
Age                   1      0.04  0.0442    1.13 0.011  0.341  
Parity                1      0.06  0.0598    1.53 0.014  0.304  
BMI                   1      0.06  0.0595    1.52 0.014  0.858  
HLA_Time_Interaction  1      0.01  0.0115    0.30 0.003  0.658  
Residuals            84      3.28  0.0390         0.785  0.484  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.3.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.96 0.018  0.810  
T1Dstatus             1      0.31  0.3066    7.85 0.073  0.044 *
Days                  1      0.01  0.0066    0.17 0.002  0.837  
seqRun                3      0.33  0.1114    2.85 0.080  0.611  
Age                   1      0.04  0.0442    1.13 0.011  0.331  
Parity                1      0.06  0.0598    1.53 0.014  0.301  
BMI                   1      0.06  0.0595    1.52 0.014  0.850  
HLA_Time_Interaction  1      0.01  0.0094    0.24 0.002  0.948  
Residuals            84      3.28  0.0391         0.786  0.534  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.3.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.95 0.018   0.81  
T1Dstatus             1      0.31  0.3066    7.83 0.073   0.07 .
Days                  1      0.01  0.0066    0.17 0.002   0.85  
seqRun                3      0.33  0.1114    2.84 0.080   0.62  
Age                   1      0.04  0.0442    1.13 0.011   0.34  
Parity                1      0.06  0.0598    1.53 0.014   0.30  
BMI                   1      0.06  0.0595    1.52 0.014   0.84  
HLA_Time_Interaction  1      0.00  0.0003    0.01 0.000   0.98  
Residuals            84      3.29  0.0392         0.788   0.51  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.3.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1      0.01  0.0123    0.32 0.003  0.687  
seqRun     3      0.39  0.1288    3.33 0.092  0.562  
Age        1      0.04  0.0374    0.97 0.009  0.605  
Parity     1      0.05  0.0533    1.38 0.013  0.309  
BMI        1      0.12  0.1178    3.04 0.028  0.337  
T1Dstatus  1      0.21  0.2123    5.48 0.051  0.095 .
HLA        2      0.07  0.0332    0.86 0.016  0.820  
Residuals 85      3.29  0.0387         0.788  0.434  
Total     95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.4 Parity

9.1.9.4.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.07  0.0373    0.97 0.018  0.796  
T1Dstatus                1      0.31  0.3066    8.00 0.073  0.045 *
Days                     1      0.01  0.0066    0.17 0.002  0.851  
seqRun                   3      0.33  0.1114    2.91 0.080  0.639  
Age                      1      0.04  0.0442    1.15 0.011  0.321  
Parity                   1      0.06  0.0598    1.56 0.014  0.284  
BMI                      1      0.06  0.0595    1.55 0.014  0.853  
Parity_Time_Interaction  1      0.07  0.0721    1.88 0.017  0.061 .
Residuals               84      3.22  0.0383         0.771  0.332  
Total                   95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.4.2 Parity (no interaction but within T1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.062  0.0310    0.68 0.059  0.595  
T1Dstatus  1     0.013  0.0129    0.29 0.012  0.829  
seqRun     1     0.086  0.0858    1.89 0.082  0.051 .
Age        1     0.036  0.0357    0.79 0.034  0.716  
BMI        1     0.018  0.0181    0.40 0.017  0.768  
Parity     1     0.148  0.1477    3.26 0.142  0.485  
Residuals 15     0.679  0.0453         0.652  0.744  
Total     22     1.041                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.4.3 Parity (no interaction but within T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.023  0.0113    0.26 0.013  0.944  
T1Dstatus  1     0.223  0.2234    5.11 0.128  0.037 *
seqRun     1     0.052  0.0518    1.18 0.030  0.926  
Age        1     0.013  0.0126    0.29 0.007  0.245  
BMI        1     0.021  0.0213    0.49 0.012  0.424  
Parity     1     0.018  0.0178    0.41 0.010  0.824  
Residuals 32     1.400  0.0437         0.800  0.556  
Total     39     1.749                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.4.4 Parity (no interaction but within T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.032  0.0161    0.41 0.024  0.853  
T1Dstatus  1     0.193  0.1932    4.93 0.142  0.028 *
seqRun     1     0.015  0.0153    0.39 0.011  0.859  
Age        1     0.028  0.0279    0.71 0.021  0.714  
BMI        1     0.035  0.0354    0.90 0.026  0.757  
Parity     1     0.073  0.0735    1.87 0.054  0.757  
Residuals 25     0.980  0.0392         0.722  0.313  
Total     32     1.357                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.5 Mode of delivery

9.1.9.5.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.99 0.018  0.820  
T1Dstatus             1      0.31  0.3066    8.11 0.073  0.054 .
MOD                   2      0.13  0.0645    1.71 0.031  0.584  
Days                  1      0.01  0.0057    0.15 0.001  0.863  
seqRun                3      0.28  0.0946    2.50 0.068  0.695  
Age                   1      0.09  0.0913    2.41 0.022  0.076 .
Parity                1      0.07  0.0653    1.73 0.016  0.290  
BMI                   1      0.09  0.0868    2.29 0.021  0.597  
MOD_Time_Interaction  1      0.03  0.0322    0.85 0.008  0.685  
Residuals            82      3.10  0.0378         0.743  0.552  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.5.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.98 0.018  0.829  
T1Dstatus             1      0.31  0.3066    8.05 0.073  0.047 *
MOD                   2      0.13  0.0645    1.69 0.031  0.572  
Days                  1      0.01  0.0057    0.15 0.001  0.881  
seqRun                3      0.28  0.0946    2.48 0.068  0.688  
Age                   1      0.09  0.0913    2.40 0.022  0.076 .
Parity                1      0.07  0.0653    1.71 0.016  0.287  
BMI                   1      0.09  0.0868    2.28 0.021  0.608  
MOD_Time_Interaction  1      0.01  0.0111    0.29 0.003  0.994  
Residuals            82      3.12  0.0381         0.748  0.729  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.5.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0373    0.99 0.018  0.817  
T1Dstatus             1      0.31  0.3066    8.09 0.073  0.059 .
MOD                   2      0.13  0.0645    1.70 0.031  0.573  
Days                  1      0.01  0.0057    0.15 0.001  0.883  
seqRun                3      0.28  0.0946    2.50 0.068  0.700  
Age                   1      0.09  0.0913    2.41 0.022  0.079 .
Parity                1      0.07  0.0653    1.72 0.016  0.281  
BMI                   1      0.09  0.0868    2.29 0.021  0.601  
MOD_Time_Interaction  1      0.03  0.0256    0.68 0.006  0.958  
Residuals            82      3.11  0.0379         0.744  0.721  
Total                95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.5.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1      0.01  0.0123    0.33 0.003  0.687  
seqRun     3      0.39  0.1288    3.41 0.092  0.563  
Age        1      0.04  0.0374    0.99 0.009  0.625  
Parity     1      0.05  0.0533    1.41 0.013  0.288  
BMI        1      0.12  0.1178    3.12 0.028  0.338  
HLA        2      0.04  0.0210    0.56 0.010  0.941  
T1Dstatus  1      0.24  0.2365    6.27 0.057  0.076 .
MOD        2      0.16  0.0787    2.09 0.038  0.476  
Residuals 83      3.13  0.0378         0.750  0.547  
Total     95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.6 Carbohydrate intake

9.1.9.6.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.07  0.0373    1.03 0.018  0.796  
T1Dstatus              1      0.31  0.3066    8.46 0.073  0.060 .
Carbs                  1      0.04  0.0403    1.11 0.010  0.611  
seqRun                 3      0.40  0.1317    3.64 0.095  0.351  
Tri                    2      0.03  0.0170    0.47 0.008  0.645  
Age                    1      0.10  0.1031    2.85 0.025  0.042 *
Parity                 1      0.08  0.0768    2.12 0.018  0.138  
BMI                    1      0.10  0.0976    2.69 0.023  0.511  
Carb_Time_Interaction  1      0.08  0.0773    2.13 0.019  0.465  
Residuals             82      2.97  0.0362         0.711  0.257  
Total                 95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.6.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.07  0.0373    1.01 0.018  0.804  
T1Dstatus              1      0.31  0.3066    8.30 0.073  0.058 .
Carbs                  1      0.04  0.0403    1.09 0.010  0.628  
seqRun                 3      0.40  0.1317    3.57 0.095  0.352  
Tri                    2      0.03  0.0170    0.46 0.008  0.644  
Age                    1      0.10  0.1031    2.79 0.025  0.051 .
Parity                 1      0.08  0.0768    2.08 0.018  0.119  
BMI                    1      0.10  0.0976    2.64 0.023  0.526  
Carb_Time_Interaction  1      0.02  0.0197    0.53 0.005  0.933  
Residuals             82      3.03  0.0369         0.725  0.431  
Total                 95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.6.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.07  0.0373    1.02 0.018  0.804  
T1Dstatus              1      0.31  0.3066    8.35 0.073  0.049 *
Carbs                  1      0.04  0.0403    1.10 0.010  0.612  
seqRun                 3      0.40  0.1317    3.59 0.095  0.332  
Tri                    2      0.03  0.0170    0.46 0.008  0.631  
Age                    1      0.10  0.1031    2.81 0.025  0.047 *
Parity                 1      0.08  0.0768    2.09 0.018  0.115  
BMI                    1      0.10  0.0976    2.66 0.023  0.536  
Carb_Time_Interaction  1      0.04  0.0387    1.05 0.009  0.697  
Residuals             82      3.01  0.0367         0.721  0.305  
Total                 95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.6.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3      0.39  0.1306    3.56 0.094  0.001 ***
Tri        2      0.04  0.0183    0.50 0.009  0.600    
Age        1      0.04  0.0381    1.04 0.009  0.589    
Parity     1      0.05  0.0527    1.43 0.013  0.583    
BMI        1      0.11  0.1075    2.93 0.026  0.577    
HLA        2      0.04  0.0196    0.53 0.009  0.948    
T1Dstatus  1      0.25  0.2509    6.83 0.060  0.085 .  
Carbs      1      0.21  0.2116    5.76 0.051  0.104    
Residuals 83      3.05  0.0367         0.730  0.238    
Total     95      4.18                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.7 Fibre intake

9.1.9.7.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.07  0.0373    0.97 0.018  0.807  
T1Dstatus               1      0.31  0.3066    7.93 0.073  0.048 *
Fiber                   1      0.00  0.0048    0.12 0.001  0.992  
seqRun                  3      0.35  0.1164    3.01 0.084  0.523  
Tri                     2      0.04  0.0193    0.50 0.009  0.595  
Age                     1      0.07  0.0658    1.70 0.016  0.176  
Parity                  1      0.07  0.0704    1.82 0.017  0.196  
BMI                     1      0.07  0.0680    1.76 0.016  0.731  
Fiber_Time_Interaction  1      0.03  0.0261    0.67 0.006  0.469  
Residuals              82      3.17  0.0387         0.760  0.547  
Total                  95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.7.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.07  0.0373    0.96 0.018  0.828  
T1Dstatus               1      0.31  0.3066    7.87 0.073  0.057 .
Fiber                   1      0.00  0.0048    0.12 0.001  0.995  
seqRun                  3      0.35  0.1164    2.99 0.084  0.511  
Tri                     2      0.04  0.0193    0.49 0.009  0.569  
Age                     1      0.07  0.0658    1.69 0.016  0.157  
Parity                  1      0.07  0.0704    1.81 0.017  0.194  
BMI                     1      0.07  0.0680    1.75 0.016  0.715  
Fiber_Time_Interaction  1      0.00  0.0040    0.10 0.001  0.950  
Residuals              82      3.19  0.0390         0.765  0.664  
Total                  95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.7.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.07  0.0373    0.96 0.018   0.80  
T1Dstatus               1      0.31  0.3066    7.90 0.073   0.05 *
Fiber                   1      0.00  0.0048    0.12 0.001   0.99  
seqRun                  3      0.35  0.1164    3.00 0.084   0.52  
Tri                     2      0.04  0.0193    0.50 0.009   0.60  
Age                     1      0.07  0.0658    1.70 0.016   0.16  
Parity                  1      0.07  0.0704    1.81 0.017   0.18  
BMI                     1      0.07  0.0680    1.75 0.016   0.72  
Fiber_Time_Interaction  1      0.02  0.0157    0.40 0.004   0.61  
Residuals              82      3.18  0.0388         0.762   0.54  
Total                  95      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.7.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3      0.39  0.1306    3.39 0.094  0.001 ***
Tri        2      0.04  0.0183    0.47 0.009  0.632    
Age        1      0.04  0.0381    0.99 0.009  0.588    
Parity     1      0.05  0.0527    1.37 0.013  0.605    
BMI        1      0.11  0.1075    2.79 0.026  0.558    
HLA        2      0.04  0.0196    0.51 0.009  0.946    
T1Dstatus  1      0.25  0.2509    6.51 0.060  0.082 .  
Fiber      1      0.06  0.0614    1.59 0.015  0.462    
Residuals 83      3.20  0.0385         0.766  0.501    
Total     95      4.18                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.8 1,5-AG (glucose control measurement)

9.1.9.8.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                   2      0.12   0.059    1.59 0.029  0.636   
T1Dstatus             1      0.37   0.368    9.89 0.091  0.035 * 
Days                  1      0.00   0.001    0.03 0.000  0.961   
seqRun                3      0.28   0.092    2.48 0.068  0.788   
Age                   1      0.06   0.065    1.74 0.016  0.273   
Parity                1      0.06   0.058    1.56 0.014  0.263   
BMI                   1      0.04   0.036    0.97 0.009  0.903   
AG15                  1      0.18   0.181    4.87 0.045  0.005 **
AG15_T1D_Interaction  1      0.08   0.078    2.11 0.019  0.400   
Residuals            77      2.86   0.037         0.708  0.162   
Total                89      4.05                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.8.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.043  0.0214    1.03 0.039  0.833  
Days       1     0.102  0.1019    4.92 0.092  0.023 *
seqRun     3     0.212  0.0706    3.41 0.191  0.575  
Age        1     0.032  0.0317    1.53 0.029  0.856  
Parity     1     0.043  0.0428    2.07 0.039  0.256  
BMI        1     0.026  0.0261    1.26 0.024  0.713  
AG15       1     0.008  0.0083    0.40 0.008  0.822  
Residuals 31     0.642  0.0207         0.580  0.381  
Total     41     1.107                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.8.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.285  0.1427    3.33 0.112  0.322  
Days       1     0.070  0.0700    1.64 0.027  0.107  
seqRun     3     0.144  0.0479    1.12 0.056  0.959  
Age        1     0.312  0.3125    7.30 0.123  0.094 .
Parity     1     0.028  0.0277    0.65 0.011  0.929  
BMI        1     0.018  0.0180    0.42 0.007  0.894  
AG15       1     0.108  0.1078    2.52 0.042  0.834  
Residuals 37     1.583  0.0428         0.621  0.873  
Total     47     2.548                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.2 Differential abundance analysis Order taxonomic level

Controlling for multiple measurements, sequencing run, conception age, BMI, parity and HLA type

       nonT1D_vs_T1D T1 T2 T3 T1_vs_T2 T2_vs_T3 T1_vs_T3 T1DT1vsT2 T1DT2vsT3 T1DT1vsT3
Down               1  1  0  0        0        1        0         0         0         0
NotSig            25 25 26 25       10       25       24         4        26        10
Up                 0  0  0  1       16        0        2        22         0        16
       noT1DT1vsT2 noT1DT2vsT3 noT1DT1vsT3
Down             0           1           0
NotSig          26          25          26
Up               0           0           0

Differentially abundant orders between T1D and non-T1D women were found. Significant differences between trimesters were also detected, however not all of the differentially abundant orders had a prevalence > 50% in one of the groups being compared or not all of them had LogFC > 0.5 or < -0.5.

Results for contrasts with significant differentially abundant orders shown below

9.2.1 Across all trimesters (T1D vs non-T1D)

     Classification  LogFC   P.Val adj.P.Val mean% Prev%
1 Enterobacteriales -0.953 0.00117    0.0305 0.146  97.9
2 Enterobacteriales -0.953 0.00117    0.0305 1.186 100.0
[1] 32

9.2.2 Only Trimester 1 (nonT1D vs T1D)

     Classification LogFC    P.Val adj.P.Val mean% Prev%
1 Enterobacteriales  -1.6 2.09e-05  0.000543 0.094   100
2 Enterobacteriales  -1.6 2.09e-05  0.000543 1.811   100

9.2.3 Only Trimester 2 (nonT1D vs T1D)

[1] "No DA taxa found"

9.2.4 Only Trimester 3 (nonT1D vs T1D)

     Classification LogFC    P.Val adj.P.Val mean% Prev%
1 Bifidobacteriales  1.57 9.12e-05   0.00237 4.058   100
2 Bifidobacteriales  1.57 9.12e-05   0.00237 0.674   100

9.2.5 T1 vs T2 (All data)

 [1] Classification LogFC          P.Val          adj.P.Val      T1:mean%      
 [6] T1Prev%        T2:mean%       T2Prev%        T3:mean%       T3Prev%       
<0 rows> (or 0-length row.names)

9.2.6 T2 vs T3 (All data)

[1] Classification LogFC          P.Val          adj.P.Val      mean%         
[6] Prev%         
<0 rows> (or 0-length row.names)

9.2.7 T1 vs T3 (All data)

 [1] Classification LogFC          P.Val          adj.P.Val      T1:mean%      
 [6] T1Prev%        T2:mean%       T2Prev%        T3:mean%       T3Prev%       
<0 rows> (or 0-length row.names)

9.2.8 T1 vs T2 (in women with T1D)

      Classification LogFC    P.Val adj.P.Val T1:mean% T1Prev% T2:mean% T2Prev%
2    Lactobacillales 0.555 0.013784   0.01792    0.192    91.7    0.244      95
4 Erysipelotrichales 0.589 0.001529   0.00234    0.093   100.0    0.082     100
7     Pasteurellales 0.645 0.000190   0.00162    0.224    66.7    0.047      80
3      Clostridiales 0.655 0.007688   0.01052   31.128   100.0   24.422     100
1   Coriobacteriales 0.677 0.021438   0.02534    1.206   100.0    1.036     100
8 Verrucomicrobiales 0.802 0.002682   0.00387    3.384   100.0    1.331     100
5    Selenomonadales 0.810 0.000704   0.00177    0.616    75.0    0.378      90
6  Enterobacteriales 0.862 0.000250   0.00162    1.811   100.0    0.963     100

9.2.9 T2 vs T3 (in women with T1D)

   Classification LogFC   P.Val adj.P.Val T2:mean% T2Prev% T3:mean% T3Prev%
1 Lactobacillales -0.54 0.00683     0.177    0.244      95    0.404     100

9.2.10 T1 vs T3 (in women with T1D)

      Classification LogFC    P.Val adj.P.Val T1:mean% T1Prev% T3:mean% T3Prev%
3     Pasteurellales 0.506 0.003865   0.02512    0.224    66.7    0.052    43.8
1  Bifidobacteriales 0.572 0.041568   0.06004    1.593    91.7    0.674   100.0
2  Enterobacteriales 0.627 0.008818   0.03928    1.811   100.0    0.996   100.0
4 Verrucomicrobiales 1.000 0.000274   0.00356    3.384   100.0    1.031   100.0

9.2.11 T1 vs T2 (in women without T1D)

[1] "No DA taxa found"

9.2.12 T2 vs T3 (in women without T1D)

     Classification  LogFC    P.Val adj.P.Val mean% Prev%
1 Bifidobacteriales -0.863 0.000306   0.00795  2.29    95
2 Bifidobacteriales -0.863 0.000306   0.00795  3.84   100

9.2.13 T1 vs T3 (in women without T1D)

     Classification  LogFC   P.Val adj.P.Val mean% Prev%
1 Bifidobacteriales -0.877 0.00205    0.0534  1.88   100
2 Bifidobacteriales -0.877 0.00205    0.0534  3.84   100

10 Phylum taxonomic level

10.1 Microbial community composition analysis at Phylum level (Beta diversity analysis)

10.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun                3      0.36   0.119    3.37 0.092  0.695  
Days                  1      0.01   0.005    0.15 0.001  0.844  
T1D_Time_Interaction  1      0.32   0.322    9.11 0.083  0.042 *
Age                   1      0.04   0.040    1.14 0.010  0.431  
Parity                1      0.06   0.057    1.62 0.015  0.635  
BMI                   1      0.05   0.054    1.52 0.014  0.847  
HLA                   2      0.05   0.025    0.70 0.013  0.846  
T1Dstatus             1      0.03   0.029    0.82 0.007  0.610  
Residuals            84      2.97   0.035         0.765  0.679  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.042

10.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
SeqRun          3     0.117  0.0390    1.08 0.120  0.349   
Nulliparous     1     0.236  0.2357    6.56 0.243  0.006 **
Age_LMP         1     0.015  0.0149    0.42 0.015  0.654   
BMI_conception  1     0.010  0.0096    0.27 0.010  0.813   
HLA.6DRML       2     0.052  0.0261    0.73 0.054  0.549   
T1Dstatus       1     0.075  0.0749    2.08 0.077  0.141   
Residuals      13     0.467  0.0359         0.481          
Total          22     0.971                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.141

Beta diversity Plot

10.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3     0.174  0.0580   1.312 0.132   0.28
Nulliparous     1     0.012  0.0121   0.275 0.009   0.74
Age_LMP         1     0.021  0.0214   0.484 0.016   0.58
BMI_conception  1     0.069  0.0686   1.553 0.052   0.22
HLA.6DRML       2     0.008  0.0038   0.086 0.006   0.99
T1Dstatus       1     0.062  0.0619   1.401 0.047   0.24
Residuals      22     0.972  0.0442         0.738       
Total          31     1.318                 1.000       
[1] 0.236

Beta diversity Plot

10.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3     0.094  0.0314    0.92 0.079  0.464  
Nulliparous     1     0.036  0.0358    1.05 0.030  0.317  
Age_LMP         1     0.030  0.0300    0.88 0.025  0.364  
BMI_conception  1     0.117  0.1170    3.44 0.098  0.056 .
HLA.6DRML       2     0.016  0.0081    0.24 0.014  0.907  
T1Dstatus       1     0.147  0.1466    4.31 0.123  0.031 *
Residuals      22     0.749  0.0340         0.630         
Total          31     1.189                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.031

Beta diversity Plot

10.1.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.061  0.0307    1.58 0.052   0.57
seqRun     3     0.244  0.0812    4.19 0.206   0.53
Age        1     0.041  0.0414    2.13 0.035   0.77
Parity     1     0.051  0.0505    2.60 0.043   0.38
BMI        1     0.022  0.0217    1.12 0.018   0.66
Days       1     0.025  0.0246    1.27 0.021   0.26
Residuals 38     0.737  0.0194         0.624   0.75
Total     47     1.180                 1.000       

Beta diversity Plot

10.1.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.061  0.0307    1.60 0.052   0.59
seqRun     3     0.244  0.0812    4.23 0.206   0.50
Age        1     0.041  0.0414    2.16 0.035   0.76
Parity     1     0.051  0.0505    2.63 0.043   0.39
BMI        1     0.022  0.0217    1.13 0.018   0.70
Tri        2     0.051  0.0255    1.33 0.043   0.22
Residuals 37     0.710  0.0192         0.602   0.64
Total     47     1.180                 1.000       

Beta diversity Plot

10.1.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.259  0.1297    3.09 0.108  0.324  
seqRun     3     0.144  0.0480    1.15 0.060  0.942  
Age        1     0.310  0.3097    7.38 0.129  0.073 .
Parity     1     0.015  0.0147    0.35 0.006  0.984  
BMI        1     0.011  0.0109    0.26 0.005  0.768  
Days       1     0.060  0.0599    1.43 0.025  0.128  
Residuals 38     1.593  0.0419         0.666  0.491  
Total     47     2.392                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

10.1.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.259  0.1297    2.99 0.108  0.337  
seqRun     3     0.144  0.0480    1.11 0.060  0.926  
Age        1     0.310  0.3097    7.14 0.129  0.081 .
Parity     1     0.015  0.0147    0.34 0.006  0.983  
BMI        1     0.011  0.0109    0.25 0.005  0.797  
Tri        2     0.048  0.0241    0.56 0.020  0.477  
Residuals 37     1.605  0.0434         0.671  0.589  
Total     47     2.392                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

10.1.9 Other factors

10.1.9.1 Age at conception

10.1.9.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.90 0.017  0.799  
T1Dstatus             1      0.29  0.2942    8.13 0.076  0.058 .
seqRun                3      0.31  0.1039    2.87 0.080  0.590  
Tri                   2      0.04  0.0182    0.50 0.009  0.582  
Age                   1      0.04  0.0376    1.04 0.010  0.346  
Parity                1      0.05  0.0547    1.51 0.014  0.591  
BMI                   1      0.05  0.0462    1.28 0.012  0.884  
Age_Time_Interaction  1      0.03  0.0317    0.88 0.008  0.314  
Residuals            83      3.00  0.0362         0.774  0.443  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.89 0.017  0.818  
T1Dstatus             1      0.29  0.2942    8.06 0.076  0.055 .
seqRun                3      0.31  0.1039    2.85 0.080  0.588  
Tri                   2      0.04  0.0182    0.50 0.009  0.587  
Age                   1      0.04  0.0376    1.03 0.010  0.338  
Parity                1      0.05  0.0547    1.50 0.014  0.606  
BMI                   1      0.05  0.0462    1.26 0.012  0.893  
Age_Time_Interaction  1      0.00  0.0045    0.12 0.001  0.846  
Residuals            83      3.03  0.0365         0.781  0.534  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.91 0.017  0.809  
T1Dstatus             1      0.29  0.2942    8.20 0.076  0.056 .
seqRun                3      0.31  0.1039    2.90 0.080  0.598  
Tri                   2      0.04  0.0182    0.51 0.009  0.588  
Age                   1      0.04  0.0376    1.05 0.010  0.349  
Parity                1      0.05  0.0547    1.52 0.014  0.593  
BMI                   1      0.05  0.0462    1.29 0.012  0.892  
Age_Time_Interaction  1      0.06  0.0550    1.53 0.014  0.142  
Residuals            83      2.98  0.0359         0.768  0.437  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.1.4 Age at conception (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.07  0.0326    0.90 0.017  0.795  
T1Dstatus  1      0.29  0.2942    8.15 0.076  0.058 .
seqRun     3      0.31  0.1039    2.88 0.080  0.609  
Tri        2      0.04  0.0182    0.50 0.009  0.596  
Parity     1      0.06  0.0577    1.60 0.015  0.487  
BMI        1      0.04  0.0388    1.07 0.010  0.880  
Age        1      0.04  0.0419    1.16 0.011  0.509  
Residuals 84      3.03  0.0361         0.782  0.477  
Total     95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.2 Body max index (BMI)

10.1.9.2.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.90 0.017  0.803  
T1Dstatus             1      0.29  0.2942    8.11 0.076  0.051 .
seqRun                3      0.31  0.1039    2.86 0.080  0.588  
Tri                   2      0.04  0.0182    0.50 0.009  0.585  
Age                   1      0.04  0.0376    1.04 0.010  0.339  
Parity                1      0.05  0.0547    1.51 0.014  0.587  
BMI                   1      0.05  0.0462    1.27 0.012  0.892  
BMI_Time_Interaction  1      0.02  0.0219    0.60 0.006  0.404  
Residuals            83      3.01  0.0363         0.776  0.450  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.2.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.89 0.017  0.770  
T1Dstatus             1      0.29  0.2942    8.06 0.076  0.071 .
seqRun                3      0.31  0.1039    2.85 0.080  0.594  
Tri                   2      0.04  0.0182    0.50 0.009  0.606  
Age                   1      0.04  0.0376    1.03 0.010  0.337  
Parity                1      0.05  0.0547    1.50 0.014  0.559  
BMI                   1      0.05  0.0462    1.26 0.012  0.895  
BMI_Time_Interaction  1      0.00  0.0037    0.10 0.001  0.819  
Residuals            83      3.03  0.0365         0.781  0.506  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.2.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.90 0.017  0.820  
T1Dstatus             1      0.29  0.2942    8.09 0.076  0.044 *
seqRun                3      0.31  0.1039    2.86 0.080  0.607  
Tri                   2      0.04  0.0182    0.50 0.009  0.547  
Age                   1      0.04  0.0376    1.03 0.010  0.336  
Parity                1      0.05  0.0547    1.51 0.014  0.623  
BMI                   1      0.05  0.0462    1.27 0.012  0.893  
BMI_Time_Interaction  1      0.02  0.0173    0.48 0.004  0.359  
Residuals            83      3.02  0.0363         0.778  0.452  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.2.4 BMI (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.07  0.0326    0.90 0.017  0.802  
T1Dstatus  1      0.29  0.2942    8.15 0.076  0.051 .
seqRun     3      0.31  0.1039    2.88 0.080  0.605  
Tri        2      0.04  0.0182    0.50 0.009  0.601  
Age        1      0.04  0.0376    1.04 0.010  0.330  
Parity     1      0.05  0.0547    1.51 0.014  0.587  
BMI        1      0.05  0.0462    1.28 0.012  0.897  
Residuals 84      3.03  0.0361         0.782  0.468  
Total     95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.3 HLA type

10.1.9.3.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.90 0.017  0.806  
T1Dstatus             1      0.29  0.2942    8.09 0.076  0.059 .
Days                  1      0.01  0.0052    0.14 0.001  0.877  
seqRun                3      0.31  0.1031    2.84 0.080  0.601  
Age                   1      0.04  0.0363    1.00 0.009  0.350  
Parity                1      0.05  0.0542    1.49 0.014  0.587  
BMI                   1      0.05  0.0521    1.43 0.013  0.867  
HLA_Time_Interaction  1      0.01  0.0096    0.27 0.002  0.350  
Residuals            84      3.05  0.0364         0.787  0.464  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.3.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.90 0.017  0.825  
T1Dstatus             1      0.29  0.2942    8.09 0.076  0.041 *
Days                  1      0.01  0.0052    0.14 0.001  0.841  
seqRun                3      0.31  0.1031    2.84 0.080  0.586  
Age                   1      0.04  0.0363    1.00 0.009  0.359  
Parity                1      0.05  0.0542    1.49 0.014  0.592  
BMI                   1      0.05  0.0521    1.43 0.013  0.862  
HLA_Time_Interaction  1      0.01  0.0105    0.29 0.003  0.879  
Residuals            84      3.05  0.0363         0.787  0.518  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.3.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.89 0.017   0.81  
T1Dstatus             1      0.29  0.2942    8.07 0.076   0.04 *
Days                  1      0.01  0.0052    0.14 0.001   0.84  
seqRun                3      0.31  0.1031    2.83 0.080   0.58  
Age                   1      0.04  0.0363    1.00 0.009   0.36  
Parity                1      0.05  0.0542    1.49 0.014   0.61  
BMI                   1      0.05  0.0521    1.43 0.013   0.90  
HLA_Time_Interaction  1      0.00  0.0021    0.06 0.001   0.97  
Residuals            84      3.06  0.0364         0.789   0.47  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.3.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
Days       1      0.01  0.0111    0.31 0.003   0.66
seqRun     3      0.35  0.1170    3.25 0.090   0.59
Age        1      0.03  0.0300    0.83 0.008   0.64
Parity     1      0.06  0.0561    1.56 0.014   0.39
BMI        1      0.12  0.1160    3.22 0.030   0.31
T1Dstatus  1      0.20  0.2028    5.63 0.052   0.11
HLA        2      0.05  0.0247    0.69 0.013   0.85
Residuals 85      3.06  0.0360         0.790   0.42
Total     95      3.88                 1.000       

10.1.9.4 Parity

10.1.9.4.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.07  0.0326    0.92 0.017  0.822  
T1Dstatus                1      0.29  0.2942    8.26 0.076  0.049 *
Days                     1      0.01  0.0052    0.14 0.001  0.859  
seqRun                   3      0.31  0.1031    2.89 0.080  0.588  
Age                      1      0.04  0.0363    1.02 0.009  0.347  
Parity                   1      0.05  0.0542    1.52 0.014  0.625  
BMI                      1      0.05  0.0521    1.46 0.013  0.870  
Parity_Time_Interaction  1      0.07  0.0714    2.00 0.018  0.046 *
Residuals               84      2.99  0.0356         0.771  0.342  
Total                   95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.4.2 Parity (no interaction but within T1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.055  0.0276    0.66 0.057   0.62  
T1Dstatus  1     0.012  0.0121    0.29 0.012   0.82  
seqRun     1     0.080  0.0796    1.89 0.082   0.05 *
Age        1     0.030  0.0298    0.71 0.031   0.72  
BMI        1     0.020  0.0200    0.48 0.021   0.79  
Parity     1     0.143  0.1434    3.41 0.148   0.43  
Residuals 15     0.631  0.0421         0.650   0.72  
Total     22     0.971                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.4.3 Parity (no interaction but within T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.020  0.0099    0.24 0.012   0.95  
T1Dstatus  1     0.212  0.2121    5.23 0.131   0.03 *
seqRun     1     0.046  0.0456    1.12 0.028   0.92  
Age        1     0.013  0.0133    0.33 0.008   0.23  
BMI        1     0.019  0.0185    0.46 0.011   0.45  
Parity     1     0.013  0.0133    0.33 0.008   0.83  
Residuals 32     1.299  0.0406         0.801   0.53  
Total     39     1.621                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.4.4 Parity (no interaction but within T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.033  0.0167    0.46 0.026  0.775  
T1Dstatus  1     0.184  0.1840    5.12 0.146  0.017 *
seqRun     1     0.012  0.0124    0.35 0.010  0.860  
Age        1     0.024  0.0241    0.67 0.019  0.716  
BMI        1     0.037  0.0368    1.02 0.029  0.771  
Parity     1     0.072  0.0716    1.99 0.057  0.782  
Residuals 25     0.899  0.0360         0.713  0.314  
Total     32     1.261                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.5 Mode of delivery

10.1.9.5.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.93 0.017  0.785  
T1Dstatus             1      0.29  0.2942    8.35 0.076  0.055 .
MOD                   2      0.11  0.0547    1.55 0.028  0.625  
Days                  1      0.00  0.0042    0.12 0.001  0.864  
seqRun                3      0.27  0.0910    2.58 0.070  0.640  
Age                   1      0.09  0.0852    2.42 0.022  0.070 .
Parity                1      0.05  0.0528    1.50 0.014  0.566  
BMI                   1      0.08  0.0779    2.21 0.020  0.638  
MOD_Time_Interaction  1      0.03  0.0293    0.83 0.008  0.734  
Residuals            82      2.89  0.0352         0.745  0.553  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.5.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.92 0.017  0.791  
T1Dstatus             1      0.29  0.2942    8.30 0.076  0.050 *
MOD                   2      0.11  0.0547    1.54 0.028  0.603  
Days                  1      0.00  0.0042    0.12 0.001  0.882  
seqRun                3      0.27  0.0910    2.57 0.070  0.619  
Age                   1      0.09  0.0852    2.40 0.022  0.086 .
Parity                1      0.05  0.0528    1.49 0.014  0.593  
BMI                   1      0.08  0.0779    2.20 0.020  0.639  
MOD_Time_Interaction  1      0.01  0.0098    0.27 0.003  0.973  
Residuals            82      2.91  0.0355         0.750  0.720  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.5.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                   2      0.07  0.0326    0.92 0.017  0.822  
T1Dstatus             1      0.29  0.2942    8.34 0.076  0.045 *
MOD                   2      0.11  0.0547    1.55 0.028  0.597  
Days                  1      0.00  0.0042    0.12 0.001  0.870  
seqRun                3      0.27  0.0910    2.58 0.070  0.639  
Age                   1      0.09  0.0852    2.41 0.022  0.066 .
Parity                1      0.05  0.0528    1.50 0.014  0.611  
BMI                   1      0.08  0.0779    2.21 0.020  0.637  
MOD_Time_Interaction  1      0.02  0.0244    0.69 0.006  0.940  
Residuals            82      2.89  0.0353         0.746  0.707  
Total                95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.5.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1      0.01  0.0111    0.31 0.003  0.697  
seqRun     3      0.35  0.1170    3.33 0.090  0.554  
Age        1      0.03  0.0300    0.85 0.008  0.614  
Parity     1      0.06  0.0561    1.60 0.014  0.395  
BMI        1      0.12  0.1160    3.30 0.030  0.328  
HLA        2      0.03  0.0153    0.43 0.008  0.956  
T1Dstatus  1      0.22  0.2217    6.30 0.057  0.084 .
MOD        2      0.15  0.0727    2.07 0.037  0.418  
Residuals 83      2.92  0.0352         0.752  0.504  
Total     95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.6 Carbohydrate intake

10.1.9.6.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.07  0.0326    0.97 0.017  0.766  
T1Dstatus              1      0.29  0.2942    8.72 0.076  0.052 .
Carbs                  1      0.03  0.0320    0.95 0.008  0.644  
seqRun                 3      0.37  0.1230    3.65 0.095  0.314  
Tri                    2      0.03  0.0160    0.48 0.008  0.650  
Age                    1      0.09  0.0914    2.71 0.024  0.053 .
Parity                 1      0.07  0.0670    1.99 0.017  0.237  
BMI                    1      0.09  0.0900    2.67 0.023  0.567  
Carb_Time_Interaction  1      0.07  0.0736    2.18 0.019  0.440  
Residuals             82      2.77  0.0337         0.713  0.252  
Total                 95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.6.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.07  0.0326    0.95 0.017  0.780  
T1Dstatus              1      0.29  0.2942    8.56 0.076  0.068 .
Carbs                  1      0.03  0.0320    0.93 0.008  0.623  
seqRun                 3      0.37  0.1230    3.58 0.095  0.329  
Tri                    2      0.03  0.0160    0.47 0.008  0.614  
Age                    1      0.09  0.0914    2.66 0.024  0.053 .
Parity                 1      0.07  0.0670    1.95 0.017  0.234  
BMI                    1      0.09  0.0900    2.62 0.023  0.556  
Carb_Time_Interaction  1      0.02  0.0199    0.58 0.005  0.921  
Residuals             82      2.82  0.0344         0.727  0.432  
Total                 95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.6.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.07  0.0326    0.95 0.017  0.790  
T1Dstatus              1      0.29  0.2942    8.62 0.076  0.062 .
Carbs                  1      0.03  0.0320    0.94 0.008  0.632  
seqRun                 3      0.37  0.1230    3.60 0.095  0.323  
Tri                    2      0.03  0.0160    0.47 0.008  0.641  
Age                    1      0.09  0.0914    2.68 0.024  0.044 *
Parity                 1      0.07  0.0670    1.96 0.017  0.201  
BMI                    1      0.09  0.0900    2.64 0.023  0.560  
Carb_Time_Interaction  1      0.04  0.0392    1.15 0.010  0.699  
Residuals             82      2.80  0.0341         0.722  0.326  
Total                 95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.6.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3      0.36  0.1190    3.48 0.092  0.001 ***
Tri        2      0.03  0.0171    0.50 0.009  0.635    
Age        1      0.03  0.0309    0.90 0.008  0.586    
Parity     1      0.06  0.0552    1.62 0.014  0.676    
BMI        1      0.11  0.1056    3.09 0.027  0.547    
HLA        2      0.03  0.0140    0.41 0.007  0.941    
T1Dstatus  1      0.24  0.2351    6.87 0.061  0.056 .  
Carbs      1      0.19  0.1948    5.69 0.050  0.092 .  
Residuals 83      2.84  0.0342         0.732  0.244    
Total     95      3.88                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.7 Fibre intake

10.1.9.7.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.07  0.0326    0.90 0.017  0.799  
T1Dstatus               1      0.29  0.2942    8.16 0.076  0.058 .
Fiber                   1      0.00  0.0031    0.09 0.001  0.977  
seqRun                  3      0.32  0.1075    2.98 0.083  0.511  
Tri                     2      0.04  0.0181    0.50 0.009  0.595  
Age                     1      0.06  0.0559    1.55 0.014  0.174  
Parity                  1      0.06  0.0621    1.72 0.016  0.332  
BMI                     1      0.06  0.0597    1.66 0.015  0.763  
Fiber_Time_Interaction  1      0.03  0.0254    0.70 0.007  0.472  
Residuals              82      2.96  0.0360         0.762  0.573  
Total                  95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.7.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.07  0.0326    0.90 0.017  0.812  
T1Dstatus               1      0.29  0.2942    8.10 0.076  0.052 .
Fiber                   1      0.00  0.0031    0.09 0.001  0.977  
seqRun                  3      0.32  0.1075    2.96 0.083  0.509  
Tri                     2      0.04  0.0181    0.50 0.009  0.607  
Age                     1      0.06  0.0559    1.54 0.014  0.166  
Parity                  1      0.06  0.0621    1.71 0.016  0.334  
BMI                     1      0.06  0.0597    1.64 0.015  0.758  
Fiber_Time_Interaction  1      0.00  0.0044    0.12 0.001  0.947  
Residuals              82      2.98  0.0363         0.767  0.631  
Total                  95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.7.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.07  0.0326    0.90 0.017  0.788  
T1Dstatus               1      0.29  0.2942    8.14 0.076  0.055 .
Fiber                   1      0.00  0.0031    0.09 0.001  0.979  
seqRun                  3      0.32  0.1075    2.97 0.083  0.509  
Tri                     2      0.04  0.0181    0.50 0.009  0.558  
Age                     1      0.06  0.0559    1.55 0.014  0.162  
Parity                  1      0.06  0.0621    1.72 0.016  0.339  
BMI                     1      0.06  0.0597    1.65 0.015  0.760  
Fiber_Time_Interaction  1      0.02  0.0175    0.48 0.005  0.561  
Residuals              82      2.96  0.0361         0.764  0.571  
Total                  95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.7.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun     3      0.36  0.1190    3.31 0.092  0.672  
Tri        2      0.03  0.0171    0.48 0.009  0.617  
Age        1      0.03  0.0309    0.86 0.008  0.568  
Parity     1      0.06  0.0552    1.54 0.014  0.692  
BMI        1      0.11  0.1056    2.94 0.027  0.551  
HLA        2      0.03  0.0140    0.39 0.007  0.964  
T1Dstatus  1      0.24  0.2351    6.54 0.061  0.094 .
Fiber      1      0.05  0.0529    1.47 0.014  0.472  
Residuals 83      2.98  0.0359         0.768  0.531  
Total     95      3.88                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.8 1,5-AG (glucose control measurement)

10.1.9.8.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
HLA                   2      0.11   0.054    1.56 0.029  0.627    
T1Dstatus             1      0.35   0.351   10.14 0.093  0.032 *  
Days                  1      0.00   0.000   -0.01 0.000  0.987    
seqRun                3      0.25   0.084    2.44 0.067  0.792    
Age                   1      0.06   0.056    1.63 0.015  0.287    
Parity                1      0.05   0.052    1.50 0.014  0.509    
BMI                   1      0.03   0.027    0.78 0.007  0.930    
AG15                  1      0.18   0.181    5.24 0.048  0.001 ***
AG15_T1D_Interaction  1      0.07   0.068    1.97 0.018  0.462    
Residuals            77      2.66   0.035         0.708  0.151    
Total                89      3.76                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.8.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.039  0.0195    1.03 0.039  0.732  
Days       1     0.092  0.0922    4.87 0.093  0.022 *
seqRun     3     0.189  0.0629    3.33 0.191  0.613  
Age        1     0.009  0.0088    0.47 0.009  0.979  
Parity     1     0.051  0.0512    2.71 0.052  0.345  
BMI        1     0.020  0.0200    1.06 0.020  0.772  
AG15       1     0.005  0.0047    0.25 0.005  0.655  
Residuals 31     0.586  0.0189         0.592  0.440  
Total     41     0.991                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.8.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.259  0.1297    3.23 0.108   0.33  
Days       1     0.070  0.0696    1.73 0.029   0.14  
seqRun     3     0.140  0.0468    1.16 0.059   0.95  
Age        1     0.304  0.3040    7.56 0.127   0.09 .
Parity     1     0.014  0.0144    0.36 0.006   0.98  
BMI        1     0.011  0.0109    0.27 0.005   0.79  
AG15       1     0.106  0.1063    2.64 0.044   0.81  
Residuals 37     1.487  0.0402         0.622   0.87  
Total     47     2.392                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.2 Differential abundance analysis Phylum taxonomic level

Controlling for multiple measurements, sequencing run, conception age, BMI, parity and HLA type

       nonT1D_vs_T1D T1 T2 T3 T1_vs_T2 T2_vs_T3 T1_vs_T3 T1DT1vsT2 T1DT2vsT3 T1DT1vsT3
Down               0  0  0  0        0        0        0         0         0         0
NotSig             8  8  7  8        8        8        8         8         8         8
Up                 0  0  1  0        0        0        0         0         0         0
       noT1DT1vsT2 noT1DT2vsT3 noT1DT1vsT3
Down             0           0           1
NotSig           8           8           7
Up               0           0           0

One differentially abundant phylum was detected between T1 and T3 only in non-T1D women.

Results for contrasts with significant differentially abundant phyla shown below

10.2.1 Across all trimesters (T1D vs non-T1D)

[1] "No DA taxa found"

10.2.2 Only Trimester 1 (nonT1D vs T1D)

[1] "No DA taxa found"

10.2.3 Only Trimester 2 (nonT1D vs T1D)

  Classification LogFC  P.Val adj.P.Val nonT1D:mean% Prev% T1D:mean% T1D:Prev%
1     Firmicutes 0.842 0.0175    0.0699         36.3   100      26.8       100

10.2.4 Only Trimester 3 (nonT1D vs T1D)

[1] "No DA taxa found"

The abundance of the Phylum Firmicutes is decreased in T1D women in comparison to non-T1D women, however, this difference is borderline significant (P=0.07).

10.2.5 T1 vs T2 (All data)

[1] "No DA taxa found"

10.2.6 T2 vs T3 (All data)

[1] "No DA taxa"

10.2.7 T1 vs T3 (All data)

[1] "No DA taxa found"

10.2.8 T1 vs T2 (in women with T1D)

[1] "No DA taxa found"

10.2.9 T2 vs T3 (in women with T1D)

[1] "No DA taxa found"

10.2.10 T1 vs T3 (in women with T1D)

[1] "No DA taxa found"

10.2.11 T1 vs T2 (in women without T1D)

[1] "No DA taxa found"

10.2.12 T2 vs T3 (in women without T1D)

[1] "No DA taxa found"

10.2.13 T1 vs T3 (in women without T1D)

  Classification LogFC   P.Val adj.P.Val mean% Prev%
1 Actinobacteria -1.17 0.00368    0.0294  2.73   100
2 Actinobacteria -1.17 0.00368    0.0294  5.64   100

10.3 Firmicutes/Bacteroides ratio (phylum taxonomic level analysis)

11 Functional analysis (Pathways)

In order to functionally annotate the metagenomic data, we used Kraken2 to filter out human genes more stringently before running HUMAnN2 again. For each sample, the HUMAnN2 output contained the following files:

  • XX_pathcoverage.tsv: This file details the abundance of each pathway in the community as a function of the abundances of the pathway’s component reactions, with each reaction’s abundance computed as the sum over abundances of genes catalyzing the reaction. Pathways with zero abundance are not included in the file. Pathway abundance is proportional to the number of complete “copies” of the pathway in the community (from the HUMAnN2 manual).

  • XX_genefamilies.tsv: This file details the abundance of each gene family in the community. Gene families are groups of evolutionarily-related protein-coding sequences that often perform similar functions. Gene family abundance at the community level is stratified to show the contributions from known and unknown species. Individual species’ abundance contributions sum to the community total abundance (from the HUMAnN2 manual).

  1. The genefamilies.csv file can contain a very large number of features depending on the complexity of your underlying sample. In order to simplify the exploration of gene family abundance data, users can regroup gene families into other functional categories (from the HUMAnN2 manual). Therefore, we regrouped our resulting gene families into MetaCyc reactions and Kegg Orthology (KO) functional categories, which has to be done in a per sample manner. Example:
  • humann2_regroup_table –input NGU5366A1_genefamilies.tsv –groups uniref90_ko –output ./NGU5366A1_genefamilies_Regrouped_KO.tsv
  1. HUMAnN2 quantifies genes and pathways in units of RPKs (reads per kilobase). These account for gene length but not sample sequencing depth. Therefore, a user will renormalize their samples prior to downstream analysis to relative abundance or copies per million (CPM) units. Both of these represent “total sum scaling (TSS)”-style normalization: in the former case, each sample is constrained to sum to 1, whereas in the latter case (CPMs) samples are constrained to sum to 1 million. Units out of 1 million are often more convenient for tables with many, many features (such as genefamilies.tsv tables). CPM as used here does not refer to unnormalized COUNTS per million, but rather copies per million. CPMs as used here are a generic analog of the TPM (transcript per million) unit in RNA-seq. You may wish to use the abbreviation CoPM for added clarity. (from the HUMAnN2 manual). We normilized the counts for each sample file for their three functional tables (XX_genefamilies.tsv, XX_genefamilies_Regrouped_KO.tsv and XX_genefamilies_Regrouped_MetaCyc.tsv) to CoPM. Example:
  • humann2_renorm_table –input NGU5366A1_genefamilies_Regrouped_KO.tsv –output NGU5366A1_genefamilies_Regrouped_KO_CoPM.tsv –units cpm
  1. Each normalized file, contained one sample. Therefore, in order to obtain a table with the functional profiles for all the samples, we need to join them into one. Example:
  • humann2_join_tables –input KO –output Pregnancy_genefamilies_KO_Rel.tsv –file_name Complete_genefamilies_Regrouped_KO_Rel.tsv
  1. The functional profiles are stratified, which means that the sum of the species abundance of a given gene gives the abundance of the gene at the community level. The stratification shows the contributions from known and unknown species to a given function. If we are interested in knowing if there is a significant difference in the abundance of a specific function at the community level (i.e. irrespective of which species is contributing to it), the abundances need to be unstratified prior to the analysis. This is done as in the following exmaple:
  • humann2_split_stratified_table –input Complete_genefamilies_Regrouped_KO_Rel.tsv –output Split/

The folder split will contain stratified and unstratified abundances.

Note: Scripts used for regrouping, normalization, joinning tables and stratification are part of HUMAnN2.

The resulting files for pathways, metacyc reactions and Kegg orthology (KO) gene categories were imported into R to process with the Phyloseq (https://github.com/joey711/phyloseq) and other packages. The analysis performed in R is described in this document.

11.1 Bar plots taxonomy

11.2 Functional Alpha diversity (Days)


Call:
geeglm(formula = Observed ~ t1dfactor * days_c + age_c + nullip + 
    bmi_c + HLA + SeqRun, data = DivCal_R_df, id = motherid, 
    corstr = "exchangeable")

 Coefficients:
                    Estimate  Std.err   Wald Pr(>|W|)    
(Intercept)         266.1375   9.5075 783.58   <2e-16 ***
t1dfactorT1D          8.6538   7.2846   1.41    0.235    
days_c                0.0825   0.0685   1.45    0.229    
age_c                 0.5975   1.0111   0.35    0.555    
nullipYes           -17.8705   7.3682   5.88    0.015 *  
bmi_c                 0.7354   0.7872   0.87    0.350    
HLADRXX               7.7104   9.6243   0.64    0.423    
HLAGroup3o4           8.5421   9.4042   0.83    0.364    
SeqRun3               9.9935   9.5574   1.09    0.296    
SeqRun4              17.7622   9.8253   3.27    0.071 .  
SeqRun6               1.5268  11.5111   0.02    0.894    
t1dfactorT1D:days_c  -0.0703   0.1093   0.41    0.520    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Estimated Scale Parameters:
            Estimate Std.err
(Intercept)     1023     150

Correlation: Structure = exchangeable  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha   0.0932   0.164
Number of clusters:   83   Maximum cluster size: 3 

No significant differences between T1D and non-T1D alpha diversity were detected.

11.3 Functional Alpha diversity (Trimesters)


Call:
geeglm(formula = Observed ~ t1dfactor * Tri + age_c + nullip + 
    bmi_c + HLA + SeqRun, data = DivCal_R_df, id = motherid, 
    corstr = "exchangeable")

 Coefficients:
                   Estimate Std.err   Wald Pr(>|W|)    
(Intercept)         257.004  12.251 440.09   <2e-16 ***
t1dfactorT1D         18.750  15.345   1.49    0.222    
TriT2                 9.800  10.021   0.96    0.328    
TriT3                15.835  12.188   1.69    0.194    
age_c                 0.713   1.002   0.51    0.477    
nullipYes           -18.025   7.356   6.00    0.014 *  
bmi_c                 0.692   0.820   0.71    0.399    
HLADRXX               8.016   9.847   0.66    0.416    
HLAGroup3o4           9.067   9.506   0.91    0.340    
SeqRun3               8.962   9.739   0.85    0.357    
SeqRun4              17.343   9.859   3.09    0.079 .  
SeqRun6               0.470  11.539   0.00    0.968    
t1dfactorT1D:TriT2  -11.512  17.483   0.43    0.510    
t1dfactorT1D:TriT3  -15.144  18.593   0.66    0.415    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Estimated Scale Parameters:
            Estimate Std.err
(Intercept)     1022     147

Correlation: Structure = exchangeable  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha    0.104   0.173
Number of clusters:   83   Maximum cluster size: 3 

11.4 Beta diversity analysis

11.4.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun                3     0.088  0.0293    1.66 0.046  0.001 ***
Days                  1     0.015  0.0153    0.87 0.008  0.149    
T1D_Time_Interaction  1     0.072  0.0719    4.07 0.037  0.101    
Age                   1     0.054  0.0544    3.08 0.028  0.994    
Parity                1     0.066  0.0658    3.72 0.034  0.115    
BMI                   1     0.022  0.0222    1.26 0.012  0.979    
HLA                   2     0.090  0.0452    2.56 0.047  0.395    
T1Dstatus             1     0.027  0.0274    1.55 0.014  0.789    
Residuals            84     1.484  0.0177         0.773  0.461    
Total                95     1.919                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.101

11.4.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3     0.060  0.0201   0.853 0.113  0.635  
Nulliparous     1     0.037  0.0370   1.570 0.069  0.134  
Age_LMP         1     0.020  0.0203   0.862 0.038  0.522  
BMI_conception  1     0.012  0.0123   0.520 0.023  0.859  
HLA.6DRML       2     0.049  0.0244   1.035 0.092  0.390  
T1Dstatus       1     0.048  0.0476   2.018 0.089  0.072 .
Residuals      13     0.306  0.0236         0.575         
Total          22     0.533                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.072

Beta diversity Plot

11.4.3 T1D status in trimester 2


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3     0.064 0.02125   1.125 0.107   0.34
Nulliparous     1     0.026 0.02553   1.352 0.043   0.21
Age_LMP         1     0.024 0.02350   1.244 0.039   0.26
BMI_conception  1     0.009 0.00856   0.453 0.014   0.94
HLA.6DRML       2     0.040 0.02004   1.061 0.067   0.38
T1Dstatus       1     0.020 0.02017   1.068 0.034   0.39
Residuals      22     0.416 0.01889         0.696       
Total          31     0.597                 1.000       
[1] 0.386

Beta diversity Plot

11.4.4 T1D status in trimester 3


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
SeqRun          3     0.045  0.0148   0.758 0.070  0.847   
Nulliparous     1     0.025  0.0248   1.266 0.039  0.197   
Age_LMP         1     0.022  0.0215   1.098 0.034  0.328   
BMI_conception  1     0.030  0.0305   1.557 0.048  0.096 . 
HLA.6DRML       2     0.035  0.0174   0.886 0.055  0.617   
T1Dstatus       1     0.046  0.0461   2.355 0.073  0.007 **
Residuals      22     0.431  0.0196         0.681          
Total          31     0.633                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.007

Beta diversity Plot

11.4.5 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.058  0.0288    1.54 0.054   0.88
seqRun     3     0.108  0.0359    1.91 0.100   0.62
Age        1     0.033  0.0332    1.77 0.031   0.87
Parity     1     0.117  0.1170    6.23 0.109   0.14
BMI        1     0.037  0.0370    1.97 0.034   0.39
Tri        2     0.029  0.0145    0.77 0.027   0.30
Residuals 37     0.695  0.0188         0.646   0.80
Total     47     1.076                 1.000       

Beta diversity Plot

11.4.6 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.075  0.0376    3.04 0.098  0.340  
seqRun     3     0.077  0.0255    2.06 0.100  0.784  
Age        1     0.082  0.0823    6.64 0.108  0.109  
Parity     1     0.021  0.0211    1.70 0.028  0.949  
BMI        1     0.030  0.0301    2.43 0.039  0.059 .
Tri        2     0.021  0.0103    0.83 0.027  0.348  
Residuals 37     0.458  0.0124         0.600  0.254  
Total     47     0.764                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

11.5 Differential abundance analysis

11.5.1 Controlling for multiple measurements, sequencing run, conception age, BMI, parity and HLA type

11.5.1.1 Results from differential abundance analysis

       nonT1D_vs_T1D  T1  T2  T3 T1_vs_T2 T2_vs_T3 T1_vs_T3 T1DT1vsT2 T1DT2vsT3 T1DT1vsT3
Down               0   0   0   3        0        0        0         0         0         0
NotSig           420 420 420 415      420      420      419       420       420       419
Up                 0   0   0   2        0        0        1         0         0         1
       noT1DT1vsT2 noT1DT2vsT3 noT1DT1vsT3
Down             2           0           0
NotSig         418         420         419
Up               0           0           1

Results for contrasts with significant differentially abundant strains shown below

11.5.2 Across all trimesters (T1D vs non-T1D)

                                                      Classification  LogFC    P.Val
1          PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I -0.714 0.000232
2 PWY-6545: pyrimidine deoxyribonucleotides de novo biosynthesis III  0.493 0.000417
  adj.P.Val nonT1D:mean% Prev% T1D:mean% T1D:Prev%
1    0.0875         45.8   100      62.7       100
2    0.0875         38.7   100      31.5       100

11.5.3 Only Trimester 1 (nonT1D vs T1D)

[1] "No DA taxa found"

11.5.4 Only Trimester 2 (nonT1D vs T1D)

[1] "No DA taxa found"

11.5.5 Only Trimester 3 (nonT1D vs T1D)

                                                                     Function  LogFC
2                                       HISDEG-PWY: L-histidine degradation I -0.933
3                   PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I -0.910
5                PWY-5695: urate biosynthesis/inosine 5-phosphate degradation -0.590
6          PWY-6545: pyrimidine deoxyribonucleotides de novo biosynthesis III  0.539
1 BRANCHED-CHAIN-AA-SYN-PWY: superpathway of branched amino acid biosynthesis  0.716
8       PWY-7357: thiamin formation from pyrithiamine and oxythiamine (yeast)  0.795
4                                     PWY-5103: L-isoleucine biosynthesis III  0.808
7                      PWY-7237: myo-, chiro- and scillo-inositol degradation  1.843
     P.Val adj.P.Val nonT1D:mean% Prev% T1D:mean% T1D:Prev%
2 1.49e-04    0.0168        0.476   100     0.706     100.0
3 8.19e-05    0.0168        0.421   100     0.653     100.0
5 2.68e-04    0.0225        0.992   100     1.379     100.0
6 1.07e-03    0.0560        0.402   100     0.312     100.0
1 1.60e-04    0.0168        1.243   100     0.804     100.0
8 7.18e-04    0.0503        0.604   100     0.379     100.0
4 1.12e-04    0.0168        1.120   100     0.683     100.0
7 1.04e-03    0.0560        0.067   100     0.020      93.8

11.5.6 T1 vs T2 (All data)

[1] "No DA taxa found"

11.5.7 T2 vs T3 (All data)

[1] "No DA taxa"

11.5.8 T1 vs T3 (All data)

                             Function LogFC    P.Val adj.P.Val mean% Prev%
1 P122-PWY: heterolactic fermentation  1.92 5.97e-06   0.00251 0.019  82.6
2 P122-PWY: heterolactic fermentation  1.92 5.97e-06   0.00251 0.014  75.0

11.5.9 T1 vs T2 (in women with T1D)

[1] Function  LogFC     P.Val     adj.P.Val T1:mean%  T1Prev%   T2:mean%  T2Prev%  
<0 rows> (or 0-length row.names)

11.5.10 T2 vs T3 (in women with T1D)

[1] Function  LogFC     P.Val     adj.P.Val T2:mean%  T2Prev%   T3:mean%  T3Prev%  
<0 rows> (or 0-length row.names)

11.5.11 T1 vs T3 (in women with T1D)

                                                                                               Function
3                           PWY0-1277: 3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation
1 HCAMHPDEG-PWY: 3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation to 2-oxopent-4-enoate
2                          PWY-6690: cinnamate and 3-hydroxycinnamate degradation to 2-oxopent-4-enoate
  LogFC   P.Val adj.P.Val T1:mean% T1Prev% T3:mean% T3Prev%
3 -1.36 0.00104    0.0731    0.005      25    0.011    56.2
1 -1.10 0.00147    0.0731    0.003      25    0.007    56.2
2 -1.10 0.00147    0.0731    0.003      25    0.007    56.2

11.5.12 T1 vs T2 (in women without T1D)

                                                   Function LogFC    P.Val adj.P.Val
2 PWY-5918: superpathay of heme biosynthesis from glutamate -1.88 0.000185    0.0399
1       HEME-BIOSYNTHESIS-II: heme biosynthesis I (aerobic) -1.80 0.000190    0.0399
  T1:mean% T1Prev% T2:mean% T2Prev%
2    0.002    18.2    0.008      75
1    0.002    27.3    0.006      95

11.5.13 T2 vs T3 (in women without T1D)

[1] "No DA taxa found"

11.5.14 T1 vs T3 (in women without T1D)

                              Function LogFC    P.Val adj.P.Val mean% Prev%
T1 P122-PWY: heterolactic fermentation  2.66 9.58e-06   0.00402 0.024  90.9
T3 P122-PWY: heterolactic fermentation  2.66 9.58e-06   0.00402 0.008  41.2
[1] 4

12 Functional analysis (Kegg Orthology)

12.1 Bar plots taxonomy

12.2 Functional Alpha diversity (Days)

12.3 Functional Alpha diversity (Trimesters)


Call:
geeglm(formula = Observed ~ t1dfactor * Tri + age_c + nullip + 
    bmi_c + HLA + SeqRun, data = DivCal_R_df, id = motherid, 
    corstr = "exchangeable")

 Coefficients:
                   Estimate Std.err   Wald Pr(>|W|)    
(Intercept)         3150.13  176.13 319.89   <2e-16 ***
t1dfactorT1D         233.53  217.71   1.15   0.2834    
TriT2                 89.77  144.02   0.39   0.5331    
TriT3                147.61  170.25   0.75   0.3859    
age_c                  6.66   13.88   0.23   0.6314    
nullipYes           -270.52  101.80   7.06   0.0079 ** 
bmi_c                  3.21   11.13   0.08   0.7730    
HLADRXX              -10.47  136.48   0.01   0.9389    
HLAGroup3o4           93.64  129.94   0.52   0.4711    
SeqRun3               -2.79  127.87   0.00   0.9826    
SeqRun4              118.31  128.05   0.85   0.3555    
SeqRun6             -167.52  150.11   1.25   0.2644    
t1dfactorT1D:TriT2  -116.05  244.44   0.23   0.6350    
t1dfactorT1D:TriT3  -176.04  254.17   0.48   0.4885    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Estimated Scale Parameters:
            Estimate Std.err
(Intercept)   195761   29111

Correlation: Structure = exchangeable  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha    0.183   0.183
Number of clusters:   83   Maximum cluster size: 3 

12.4 Beta diversity analysis

12.4.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun                3     0.157  0.0524    2.10 0.057  0.001 ***
Days                  1     0.025  0.0248    0.99 0.009  0.121    
T1D_Time_Interaction  1     0.121  0.1207    4.83 0.044  0.044 *  
Age                   1     0.088  0.0880    3.52 0.032  0.993    
Parity                1     0.070  0.0703    2.81 0.025  0.212    
BMI                   1     0.050  0.0503    2.01 0.018  0.982    
HLA                   2     0.133  0.0665    2.66 0.048  0.334    
T1Dstatus             1     0.031  0.0307    1.23 0.011  0.940    
Residuals            84     2.099  0.0250         0.757  0.428    
Total                95     2.774                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.044

12.4.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3     0.082  0.0275   0.815 0.111  0.761  
Nulliparous     1     0.038  0.0375   1.112 0.051  0.375  
Age_LMP         1     0.040  0.0402   1.191 0.054  0.301  
BMI_conception  1     0.026  0.0259   0.769 0.035  0.671  
HLA.6DRML       2     0.063  0.0317   0.940 0.086  0.584  
T1Dstatus       1     0.053  0.0528   1.565 0.071  0.098 .
Residuals      13     0.439  0.0337         0.592         
Total          22     0.741                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.098

Beta diversity Plot

12.4.3 T1D status in trimester 2


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3     0.096  0.0320    1.20 0.111  0.219  
Nulliparous     1     0.042  0.0425    1.59 0.049  0.096 .
Age_LMP         1     0.035  0.0347    1.30 0.040  0.221  
BMI_conception  1     0.019  0.0194    0.73 0.022  0.664  
HLA.6DRML       2     0.057  0.0287    1.08 0.066  0.363  
T1Dstatus       1     0.031  0.0313    1.18 0.036  0.307  
Residuals      22     0.586  0.0266         0.675         
Total          31     0.867                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.307

Beta diversity Plot

12.4.4 T1D status in trimester 3


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
SeqRun          3     0.077  0.0258   0.906 0.082  0.617   
Nulliparous     1     0.030  0.0302   1.058 0.032  0.355   
Age_LMP         1     0.037  0.0367   1.286 0.039  0.230   
BMI_conception  1     0.044  0.0438   1.534 0.046  0.102   
HLA.6DRML       2     0.059  0.0295   1.035 0.062  0.406   
T1Dstatus       1     0.073  0.0733   2.570 0.077  0.008 **
Residuals      22     0.627  0.0285         0.662          
Total          31     0.948                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.008

Beta diversity Plot

12.4.5 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.111  0.0555    2.37 0.079   0.51
seqRun     3     0.156  0.0521    2.22 0.112   0.66
Age        1     0.050  0.0505    2.15 0.036   0.93
Parity     1     0.090  0.0901    3.84 0.064   0.27
BMI        1     0.080  0.0803    3.42 0.057   0.17
Tri        2     0.042  0.0209    0.89 0.030   0.28
Residuals 37     0.868  0.0235         0.621   0.73
Total     47     1.398                 1.000       

Beta diversity Plot

12.4.6 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.134  0.0670    3.26 0.107   0.32
seqRun     3     0.162  0.0540    2.62 0.129   0.87
Age        1     0.102  0.1018    4.95 0.081   0.13
Parity     1     0.028  0.0283    1.38 0.023   0.96
BMI        1     0.038  0.0383    1.86 0.031   0.18
Tri        2     0.026  0.0128    0.62 0.020   0.57
Residuals 37     0.761  0.0206         0.608   0.61
Total     47     1.251                 1.000       

Beta diversity Plot

12.5 Differential abundance analysis

Controlling for multiple measurements, sequencing run, conception age, BMI, parity and HLA type

       nonT1D_vs_T1D   T1   T2   T3 T1_vs_T2 T2_vs_T3 T1_vs_T3 T1DT1vsT2 T1DT2vsT3
Down               0    0    0    3        0        0        5         1         0
NotSig          5480 5480 5480 5421     5470     5480     5421      4846      5480
Up                 0    0    0   56       10        0       54       633         0
       T1DT1vsT3 noT1DT1vsT2 noT1DT2vsT3 noT1DT1vsT3
Down          30           0           0          10
NotSig      4838        5474        5480        5440
Up           612           6           0          30

Results for contrasts with significant differentially abundant strains shown below

12.5.1 Across all trimesters (T1D vs non-T1D)

  Classification LogFC    P.Val adj.P.Val nonT1D:mean% Prev% T1D:mean% T1D:Prev%
3         K08681  1.13 5.20e-05    0.0894        1.963 100.0     0.823     100.0
5         K13788  1.34 4.21e-05    0.0894        0.276  93.8     0.091      83.3
1         K03465  1.37 7.95e-05    0.0894        2.694 100.0     1.429     100.0
2         K04092  1.52 8.16e-05    0.0894        0.420  70.8     0.081      39.6
4         K09163  1.74 7.16e-05    0.0894        0.808 100.0     0.252      95.8

12.5.2 Only Trimester 1 (nonT1D vs T1D)

  Function  LogFC    P.Val adj.P.Val nonT1D:mean% Prev% T1D:mean% T1D:Prev%
1   K03815 -1.229 5.91e-05    0.0540            0  50.0     0.001      50.0
3   K10986 -1.034 4.57e-05    0.0540            0  43.8     0.000      56.2
4   K15721 -1.030 1.02e-04    0.0623            0  31.2     0.000      56.2
2   K04784 -0.961 2.81e-05    0.0540            0  31.2     0.000      56.2

12.5.3 Only Trimester 2 (nonT1D vs T1D)

[1] "No DA taxa found"

12.5.4 Only Trimester 3 (nonT1D vs T1D)

    Function  LogFC    P.Val adj.P.Val nonT1D:mean% Prev% T1D:mean% T1D:Prev%
74    K02852 -2.314 3.22e-04  0.043062        0.007  81.2     0.024     100.0
21    K00936 -2.093 5.10e-04  0.048661        0.004  87.5     0.007      93.8
100   K04045 -1.622 8.57e-04  0.059982        0.000  81.2     0.002      93.8
93    K03735 -1.560 2.33e-03  0.084572        0.001 100.0     0.003     100.0
186   K13630 -1.316 3.54e-03  0.098070        0.001  18.8     0.002      50.0
110   K05834 -1.316 2.45e-03  0.085689        0.001  43.8     0.002      62.5
5     K00242 -1.297 1.52e-03  0.073171        0.001  50.0     0.002      56.2
204   K19000 -1.259 9.94e-04  0.062435        0.000  37.5     0.001      62.5
182   K12524 -1.237 2.96e-03  0.091623        0.004 100.0     0.008     100.0
142   K07443 -1.232 3.82e-03  0.099601        0.013 100.0     0.020     100.0
122   K06891 -1.217 2.51e-03  0.085851        0.001  56.2     0.002      56.2
16    K00832 -1.215 2.62e-03  0.086178        0.000  62.5     0.001      75.0
203   K18929 -1.158 1.46e-03  0.072717        0.013 100.0     0.025     100.0
10    K00568 -1.133 3.79e-03  0.099601        0.001  56.2     0.002      56.2
103   K04334 -1.059 5.82e-04  0.052949        0.000  43.8     0.001      62.5
175   K10973 -1.054 3.53e-03  0.098070        0.000  50.0     0.001      62.5
145   K07470 -1.049 2.82e-03  0.088368        0.000  43.8     0.002      68.8
151   K07803 -1.026 1.70e-03  0.073171        0.000  43.8     0.002      62.5
107   K05367 -1.024 7.08e-04  0.054892        0.016 100.0     0.026     100.0
162   K09712 -1.020 1.33e-03  0.072717        0.000  25.0     0.001      56.2
195   K16326 -1.020 1.76e-03  0.073171        0.000  43.8     0.001      62.5
137   K07165 -0.975 1.45e-03  0.072717        0.000  31.2     0.001      50.0
64    K02394 -0.961 2.26e-03  0.083500        0.000  56.2     0.001      68.8
39    K01483 -0.959 2.44e-03  0.085689        0.000  31.2     0.001      56.2
91    K03668 -0.954 3.77e-03  0.099601        0.000  31.2     0.001      56.2
69    K02565 -0.943 3.71e-03  0.099601        0.000  56.2     0.001      81.2
113   K05984 -0.928 2.19e-03  0.082593        0.000  56.2     0.001      75.0
172   K10680 -0.918 2.70e-03  0.086178        0.000  56.2     0.001      68.8
98    K04024 -0.908 1.55e-03  0.073171        0.000  50.0     0.001      81.2
198   K17247 -0.899 3.06e-03  0.091623        0.000  56.2     0.001      68.8
46    K01791 -0.867 2.46e-04  0.040944        0.037 100.0     0.068     100.0
154   K08162 -0.853 1.22e-03  0.068945        0.000  56.2     0.001      62.5
20    K00929 -0.814 1.87e-03  0.075508        0.044 100.0     0.067     100.0
78    K03281 -0.805 2.41e-03  0.085689        0.054 100.0     0.078     100.0
181   K12343 -0.789 2.64e-03  0.086178        0.040 100.0     0.058     100.0
201   K18691 -0.787 1.79e-03  0.073171        0.037 100.0     0.057     100.0
97    K03832 -0.753 3.63e-03  0.099102        0.068 100.0     0.111     100.0
38    K01468 -0.740 3.79e-03  0.099601        0.052 100.0     0.080     100.0
83    K03474 -0.726 1.79e-03  0.073171        0.046 100.0     0.067     100.0
99    K04032 -0.676 3.35e-03  0.095030        0.000  50.0     0.001      56.2
95    K03771 -0.675 3.03e-03  0.091623        0.048 100.0     0.071     100.0
75    K03118 -0.669 1.99e-03  0.079203        0.048 100.0     0.069     100.0
43    K01719 -0.668 2.70e-03  0.086178        0.049 100.0     0.071     100.0
180   K12137 -0.662 3.58e-03  0.098621        0.000  62.5     0.001      68.8
96    K03797 -0.561 1.98e-03  0.079203        0.154 100.0     0.220     100.0
128   K06997  0.564 3.06e-03  0.091623        0.050 100.0     0.040     100.0
31    K01129  0.603 3.00e-03  0.091623        0.050 100.0     0.040     100.0
61    K02110  0.650 1.15e-03  0.067899        0.164 100.0     0.121     100.0
14    K00763  0.654 2.63e-03  0.086178        0.055 100.0     0.044     100.0
44    K01756  0.745 2.63e-03  0.086178        0.074 100.0     0.055     100.0
60    K02108  0.782 1.10e-03  0.066047        0.065 100.0     0.043     100.0
140   K07317  0.811 2.12e-03  0.081547        0.001  56.2     0.000      37.5
56    K02037  0.813 1.09e-03  0.066047        0.044 100.0     0.028     100.0
120   K06608  0.845 1.50e-03  0.073171        0.001  50.0     0.000      50.0
133   K07040  0.857 2.67e-03  0.086178        0.035 100.0     0.019     100.0
17    K00868  0.878 5.20e-04  0.048661        0.043 100.0     0.026     100.0
23    K00941  0.887 2.76e-04  0.040944        0.055 100.0     0.038     100.0
136   K07090  0.907 1.76e-03  0.073171        0.043 100.0     0.030     100.0
124   K06958  0.918 2.70e-03  0.086178        0.024 100.0     0.013     100.0
101   K04066  0.933 1.16e-03  0.067899        0.033 100.0     0.019     100.0
177   K11189  0.936 2.18e-03  0.082593        0.105 100.0     0.067     100.0
11    K00611  0.941 6.52e-04  0.054892        0.081 100.0     0.055     100.0
19    K00897  0.979 2.70e-03  0.086178        0.001  50.0     0.000      31.2
76    K03151  1.002 3.54e-03  0.098070        0.038 100.0     0.024     100.0
15    K00821  1.006 2.72e-03  0.086298        0.040 100.0     0.027     100.0
25    K00975  1.025 1.55e-03  0.073171        0.101 100.0     0.065     100.0
123   K06901  1.027 1.25e-03  0.068945        0.049 100.0     0.031     100.0
89    K03574  1.034 1.58e-04  0.040944        0.075 100.0     0.040     100.0
146   K07574  1.036 2.01e-03  0.079333        0.042 100.0     0.029     100.0
77    K03216  1.043 5.24e-04  0.048661        0.040 100.0     0.024     100.0
163   K09747  1.048 2.08e-03  0.081394        0.048 100.0     0.029     100.0
134   K07042  1.051 7.83e-04  0.056484        0.041 100.0     0.025     100.0
164   K09762  1.054 3.69e-03  0.099601        0.024 100.0     0.012     100.0
105   K04488  1.057 2.22e-03  0.082723        0.059 100.0     0.036     100.0
114   K06024  1.057 3.81e-03  0.099601        0.025 100.0     0.014     100.0
143   K07454  1.062 2.75e-04  0.040944        0.001  68.8     0.000      43.8
153   K07979  1.066 2.13e-03  0.081547        0.058 100.0     0.032     100.0
118   K06346  1.066 3.44e-03  0.096738        0.025 100.0     0.015     100.0
45    K01786  1.071 3.28e-03  0.093698        0.032 100.0     0.015     100.0
49    K01996  1.074 3.02e-03  0.091623        0.055 100.0     0.034     100.0
111   K05896  1.082 1.43e-03  0.072717        0.020 100.0     0.012     100.0
169   K10117  1.089 2.47e-03  0.085689        0.075 100.0     0.041     100.0
51    K02026  1.093 1.82e-03  0.073942        0.077 100.0     0.050     100.0
50    K02025  1.094 1.60e-03  0.073171        0.060 100.0     0.035     100.0
106   K04758  1.103 1.22e-03  0.068945        0.095 100.0     0.053     100.0
53    K02028  1.110 2.44e-04  0.040944        0.085 100.0     0.045     100.0
190   K15023  1.116 2.36e-03  0.084897        0.003 100.0     0.001      87.5
30    K01090  1.120 3.10e-03  0.091891        0.015 100.0     0.006     100.0
22    K00937  1.122 2.45e-04  0.040944        0.029 100.0     0.015     100.0
87    K03523  1.124 1.39e-03  0.072717        0.029 100.0     0.016     100.0
168   K10112  1.126 4.05e-04  0.045251        0.081 100.0     0.046     100.0
165   K09772  1.132 1.35e-03  0.072717        0.030 100.0     0.016     100.0
58    K02072  1.132 2.68e-03  0.086178        0.037 100.0     0.023     100.0
104   K04487  1.134 4.15e-04  0.045251        0.047 100.0     0.027     100.0
116   K06200  1.135 5.99e-04  0.052949        0.039 100.0     0.023     100.0
125   K06960  1.140 7.11e-04  0.054892        0.070 100.0     0.037     100.0
159   K08884  1.141 1.65e-03  0.073171        0.034 100.0     0.017     100.0
174   K10907  1.147 7.34e-04  0.055082        0.051 100.0     0.028     100.0
18    K00878  1.148 3.49e-04  0.043062        0.039 100.0     0.019     100.0
55    K02030  1.150 2.61e-04  0.040944        0.080 100.0     0.043     100.0
152   K07816  1.160 2.29e-03  0.083671        0.046 100.0     0.018     100.0
81    K03338  1.161 1.85e-04  0.040944        0.002  75.0     0.000      37.5
92    K03724  1.165 4.35e-04  0.045251        0.003 100.0     0.000      93.8
24    K00965  1.172 3.54e-04  0.043062        0.030 100.0     0.016     100.0
27    K00995  1.174 3.44e-05  0.019424        0.096 100.0     0.046     100.0
41    K01693  1.176 2.17e-04  0.040944        0.051 100.0     0.027     100.0
112   K05967  1.189 8.87e-04  0.059982        0.002  75.0     0.000      68.8
160   K09157  1.192 6.80e-04  0.054892        0.061 100.0     0.034     100.0
129   K07003  1.195 8.68e-04  0.059982        0.027 100.0     0.012     100.0
148   K07738  1.199 1.37e-04  0.040944        0.044 100.0     0.020     100.0
66    K02433  1.202 2.56e-04  0.040944        0.039 100.0     0.017     100.0
36    K01356  1.205 1.77e-04  0.040944        0.083 100.0     0.050     100.0
29    K01026  1.208 2.87e-03  0.089323        0.002  62.5     0.000      50.0
12    K00620  1.221 1.93e-04  0.040944        0.051 100.0     0.030     100.0
52    K02027  1.222 2.02e-04  0.040944        0.057 100.0     0.029     100.0
156   K08316  1.231 2.09e-03  0.081394        0.015 100.0     0.006     100.0
119   K06378  1.232 3.15e-03  0.092240        0.014 100.0     0.007     100.0
48    K01989  1.233 2.48e-03  0.085689        0.048 100.0     0.025     100.0
144   K07467  1.233 1.54e-03  0.073171        0.005  93.8     0.001      87.5
1     K00008  1.239 1.24e-03  0.068945        0.020 100.0     0.009     100.0
178   K11358  1.239 1.02e-03  0.063002        0.035 100.0     0.021     100.0
202   K18828  1.244 3.20e-03  0.092738        0.006 100.0     0.001      81.2
109   K05832  1.247 3.72e-03  0.099601        0.027 100.0     0.011     100.0
67    K02434  1.254 1.34e-04  0.040944        0.044 100.0     0.020     100.0
170   K10118  1.260 8.83e-04  0.059982        0.064 100.0     0.032     100.0
32    K01193  1.275 1.00e-03  0.062435        0.049 100.0     0.025     100.0
171   K10119  1.287 6.55e-04  0.054892        0.065 100.0     0.030     100.0
68    K02435  1.289 3.52e-04  0.043062        0.038 100.0     0.016     100.0
184   K13570  1.289 1.57e-03  0.073171        0.003  56.2     0.000      18.8
37    K01439  1.296 1.66e-03  0.073171        0.024 100.0     0.013     100.0
85    K03488  1.313 2.20e-03  0.082593        0.026 100.0     0.013     100.0
2     K00016  1.327 1.65e-03  0.073171        0.025 100.0     0.009     100.0
7     K00375  1.329 3.72e-04  0.044315        0.022 100.0     0.011     100.0
88    K03529  1.335 1.57e-03  0.073171        0.006 100.0     0.002     100.0
126   K06972  1.336 1.46e-03  0.072717        0.010 100.0     0.004     100.0
138   K07166  1.348 3.29e-04  0.043062        0.044 100.0     0.024     100.0
132   K07033  1.364 3.76e-03  0.099601        0.009 100.0     0.004     100.0
54    K02029  1.414 2.23e-05  0.015257        0.101 100.0     0.041     100.0
70    K02588  1.427 1.41e-03  0.072717        0.005  93.8     0.001      93.8
57    K02049  1.433 2.49e-03  0.085689        0.018 100.0     0.006     100.0
90    K03660  1.438 1.65e-03  0.073171        0.009 100.0     0.004     100.0
80    K03337  1.445 1.69e-03  0.073171        0.004  93.8     0.002     100.0
9     K00563  1.450 1.76e-03  0.073171        0.029 100.0     0.011     100.0
147   K07726  1.454 2.58e-03  0.086178        0.016 100.0     0.005     100.0
86    K03518  1.464 2.14e-04  0.040944        0.018 100.0     0.008     100.0
158   K08681  1.471 7.21e-06  0.007215        0.024 100.0     0.007     100.0
65    K02406  1.479 1.76e-03  0.073171        0.035 100.0     0.012     100.0
28    K00997  1.480 5.02e-04  0.048661        0.024 100.0     0.008     100.0
4     K00209  1.483 1.70e-03  0.073171        0.006  87.5     0.000      56.2
115   K06042  1.485 7.60e-05  0.032777        0.018 100.0     0.007     100.0
71    K02744  1.486 2.54e-03  0.086178        0.004  93.8     0.001      87.5
199   K17686  1.506 8.63e-04  0.059982        0.013 100.0     0.004     100.0
35    K01354  1.508 1.40e-03  0.072717        0.004  87.5     0.001      93.8
205   K19310  1.517 1.82e-04  0.040944        0.036 100.0     0.014     100.0
82    K03465  1.523 1.56e-04  0.040944        0.031 100.0     0.014     100.0
121   K06859  1.525 7.82e-04  0.056484        0.003  87.5     0.000      62.5
73    K02851  1.530 3.01e-03  0.091623        0.009 100.0     0.003     100.0
63    K02203  1.539 2.97e-04  0.042834        0.014 100.0     0.005     100.0
117   K06215  1.541 8.95e-06  0.007215        0.034 100.0     0.013     100.0
94    K03767  1.544 3.41e-03  0.096268        0.011 100.0     0.003     100.0
131   K07012  1.549 5.95e-04  0.052949        0.009 100.0     0.005     100.0
40    K01494  1.555 4.43e-04  0.045251        0.013 100.0     0.004     100.0
13    K00690  1.566 2.60e-04  0.040944        0.015 100.0     0.006     100.0
141   K07442  1.576 3.15e-03  0.092240        0.006  93.8     0.001     100.0
127   K06987  1.582 1.18e-03  0.068215        0.010 100.0     0.004     100.0
84    K03484  1.593 7.10e-04  0.054892        0.018 100.0     0.005     100.0
176   K11050  1.593 1.12e-03  0.066773        0.011 100.0     0.004      93.8
193   K16209  1.613 2.37e-03  0.084897        0.006  87.5     0.001     100.0
197   K16925  1.616 1.37e-03  0.072717        0.005  87.5     0.001      93.8
173   K10805  1.650 3.63e-03  0.099102        0.005  93.8     0.001      81.2
33    K01198  1.657 7.08e-04  0.054892        0.027 100.0     0.007     100.0
200   K17810  1.660 3.89e-04  0.045251        0.004 100.0     0.001     100.0
183   K13527  1.661 1.60e-03  0.073171        0.006  87.5     0.001      93.8
167   K10008  1.689 3.24e-03  0.093574        0.007  93.8     0.002     100.0
161   K09163  1.694 7.64e-04  0.056484        0.009 100.0     0.003     100.0
6     K00324  1.711 2.29e-03  0.083671        0.011 100.0     0.003     100.0
179   K11928  1.720 7.73e-06  0.007215        0.035 100.0     0.013     100.0
192   K16148  1.724 1.37e-03  0.072717        0.006  87.5     0.001      93.8
139   K07260  1.725 7.02e-04  0.054892        0.028 100.0     0.012     100.0
79    K03335  1.725 8.37e-05  0.032777        0.004  81.2     0.001      62.5
108   K05794  1.740 4.21e-04  0.045251        0.005  87.5     0.001      93.8
194   K16235  1.780 1.62e-03  0.073171        0.007  87.5     0.001      87.5
157   K08372  1.815 4.16e-04  0.045251        0.009 100.0     0.002     100.0
166   K10007  1.826 9.35e-04  0.062148        0.006  87.5     0.001     100.0
149   K07768  1.829 9.62e-04  0.062148        0.007  87.5     0.001      93.8
8     K00395  1.840 2.64e-04  0.040944        0.009 100.0     0.003     100.0
150   K07776  1.843 9.45e-04  0.062148        0.006  93.8     0.002      93.8
3     K00171  1.857 9.22e-06  0.007215        0.006  93.8     0.001      87.5
185   K13571  1.859 7.24e-04  0.055082        0.007  87.5     0.001     100.0
42    K01697  1.868 9.98e-04  0.062435        0.007  87.5     0.001      93.8
59    K02077  1.873 9.64e-04  0.062148        0.011 100.0     0.002     100.0
135   K07080  1.873 3.28e-04  0.043062        0.010 100.0     0.002     100.0
187   K13787  1.903 8.22e-05  0.032777        0.010 100.0     0.002     100.0
130   K07006  1.930 1.78e-03  0.073171        0.008  87.5     0.001      81.2
26    K00990  1.943 1.06e-06  0.002904        0.004  75.0     0.000      56.2
47    K01807  2.008 1.97e-04  0.040944        0.014 100.0     0.003     100.0
155   K08300  2.015 4.46e-04  0.045251        0.009  87.5     0.000      87.5
72    K02822  2.024 5.09e-04  0.048661        0.006 100.0     0.001      93.8
189   K13940  2.029 1.37e-04  0.040944        0.008 100.0     0.001     100.0
62    K02122  2.064 3.50e-04  0.043062        0.010  87.5     0.001      87.5
188   K13788  2.070 1.30e-07  0.000712        0.003 100.0     0.000      68.8
102   K04092  2.114 3.39e-06  0.006184        0.006  68.8     0.000      31.2
196   K16784  2.280 1.04e-04  0.037979        0.010  87.5     0.001     100.0
191   K16147  2.384 3.54e-05  0.019424        0.009  87.5     0.000      81.2
34    K01304  2.432 5.61e-05  0.027927        0.007  81.2     0.000      62.5

12.5.5 T1 vs T2 (All data)

  Function LogFC    P.Val adj.P.Val T1:mean% T1Prev% T2:mean% T2Prev% T3:mean% T3Prev%
1   K02339 0.502 3.09e-05  0.024195    0.001    60.9    0.000    32.5        0    21.2
2   K02471 0.580 1.05e-04  0.052281    0.002    91.3    0.001    82.5        0    57.6
3   K05589 0.619 3.15e-04  0.096449    0.002    65.2    0.000    42.5        0    27.3
4   K06212 0.589 8.53e-08  0.000234    0.001    69.6    0.000    45.0        0    36.4
5   K07234 0.628 7.49e-08  0.000234    0.001    78.3    0.000    55.0        0    36.4
6   K09780 0.503 1.87e-04  0.068223    0.001    56.5    0.000    25.0        0    21.2
7   K09801 0.640 9.98e-07  0.001367    0.001    69.6    0.000    32.5        0    27.3

12.5.6 T2 vs T3 (All data)

[1] "No DA taxa"

12.5.7 T1 vs T3 (All data)

   Function  LogFC    P.Val adj.P.Val T1:mean% T1Prev% T2:mean% T2Prev% T3:mean% T3Prev%
1    K00368  0.655 7.03e-08  4.14e-05    0.001    65.2    0.000    60.0    0.000    30.3
2    K00955  1.104 3.43e-05  6.95e-03    0.003    69.6    0.001    47.5    0.001    57.6
3    K01166  0.703 1.74e-07  6.79e-05    0.001    69.6    0.000    52.5    0.000    33.3
4    K01226 -0.790 6.37e-04  5.64e-02    0.002    87.0    0.002    95.0    0.002   100.0
5    K01668  0.563 9.89e-08  4.93e-05    0.000    73.9    0.000    50.0    0.000    33.3
6    K01674  0.678 1.05e-05  2.73e-03    0.001    69.6    0.000    45.0    0.000    33.3
7    K02012  0.962 1.29e-04  1.81e-02    0.003    78.3    0.002    80.0    0.001    75.8
8    K02062  0.768 3.00e-06  8.21e-04    0.001    82.6    0.000    67.5    0.000    48.5
9    K02339  0.584 1.95e-06  5.95e-04    0.001    60.9    0.000    32.5    0.000    21.2
10   K02344  0.568 8.13e-05  1.27e-02    0.001    60.9    0.000    32.5    0.000    27.3
11   K02471  0.938 4.05e-09  5.03e-06    0.002    91.3    0.001    82.5    0.000    57.6
12   K02496  0.643 2.42e-04  3.04e-02    0.001    91.3    0.001    80.0    0.000    69.7
13   K02554 -0.597 1.21e-04  1.79e-02    0.000    47.8    0.001    42.5    0.001    63.6
14   K03074  0.817 6.34e-05  1.09e-02    0.003    87.0    0.003    82.5    0.002    57.6
15   K03656  0.700 1.89e-05  4.31e-03    0.001    91.3    0.001    77.5    0.000    63.6
16   K03923  0.621 7.75e-04  6.27e-02    0.001    73.9    0.001    77.5    0.000    69.7
17   K04073 -0.532 3.03e-04  3.33e-02    0.000    43.5    0.001    47.5    0.001    60.6
18   K05589  0.896 5.40e-07  1.85e-04    0.002    65.2    0.000    42.5    0.000    27.3
19   K05685  0.618 4.59e-09  5.03e-06    0.000    82.6    0.000    57.5    0.000    33.3
20   K06194  0.549 3.92e-05  7.42e-03    0.001    82.6    0.000    67.5    0.000    78.8
21   K06212  0.696 9.11e-10  1.66e-06    0.001    69.6    0.000    45.0    0.000    36.4
22   K07084  0.500 2.20e-06  6.35e-04    0.001    65.2    0.000    60.0    0.000    36.4
23   K07121  0.525 1.03e-03  7.46e-02    0.001    82.6    0.001    82.5    0.000    72.7
24   K07234  0.846 8.71e-12  4.78e-08    0.001    78.3    0.000    55.0    0.000    36.4
25   K07803 -0.627 1.63e-04  2.24e-02    0.000    13.0    0.001    37.5    0.001    51.5
26   K08310  0.623 6.38e-04  5.64e-02    0.002    69.6    0.001    60.0    0.001    60.6
27   K09780  0.575 2.76e-05  6.05e-03    0.001    56.5    0.000    25.0    0.000    21.2
28   K09801  0.857 5.55e-10  1.52e-06    0.001    69.6    0.000    32.5    0.000    27.3
29   K09824  0.722 3.03e-05  6.38e-03    0.001    73.9    0.001    72.5    0.000    63.6
30   K11211  0.700 1.59e-08  1.24e-05    0.001    73.9    0.000    50.0    0.000    27.3
31   K11605  0.687 3.73e-04  3.78e-02    0.001    87.0    0.001    72.5    0.000    60.6
32   K11606  0.574 6.78e-04  5.89e-02    0.001    78.3    0.000    75.0    0.000    57.6
33   K11607  0.596 1.08e-06  3.49e-04    0.001    65.2    0.000    60.0    0.000    30.3
34   K12982  0.696 1.39e-07  5.88e-05    0.001    65.2    0.000    55.0    0.000    30.3
35   K12984  0.575 3.93e-05  7.42e-03    0.001    65.2    0.000    57.5    0.000    33.3
36   K13634  0.678 1.33e-08  1.21e-05    0.001    60.9    0.000    52.5    0.000    27.3
37   K15461  0.576 7.55e-08  4.14e-05    0.001    87.0    0.000    75.0    0.000    54.5
38   K15984  0.650 8.79e-05  1.34e-02    0.001    69.6    0.001    55.0    0.000    27.3
39   K17733  1.330 3.11e-04  3.33e-02    0.005    60.9    0.002    55.0    0.002    54.5
40   K18893  0.598 4.25e-07  1.55e-04    0.001    69.6    0.000    67.5    0.000    33.3
41   K19509 -0.530 3.81e-04  3.80e-02    0.000    43.5    0.001    57.5    0.001    57.6

12.5.8 T1 vs T2 (in women with T1D)

   Function  LogFC    P.Val adj.P.Val T1:mean% T1Prev% T2:mean% T2Prev%
70   K18120 -0.748 3.22e-03   0.03288    0.001   100.0    0.002     100
60   K09740 -0.677 1.18e-02   0.08868    0.002   100.0    0.004     100
51   K07034 -0.662 7.61e-03   0.06236    0.000    50.0    0.001      70
7    K00782 -0.563 1.05e-02   0.08017    0.032   100.0    0.045     100
44   K04784  0.502 4.55e-04   0.01253    0.001    58.3    0.000      60
32   K03216  0.518 1.36e-02   0.09912    0.032   100.0    0.026     100
13   K01355  0.534 2.82e-04   0.01182    0.001    58.3    0.000      50
73   K18893  0.535 5.97e-04   0.01319    0.001    58.3    0.000      65
53   K07090  0.542 7.87e-03   0.06411    0.039   100.0    0.027     100
66   K14170  0.553 9.39e-03   0.07372    0.022   100.0    0.017     100
54   K07478  0.559 2.33e-03   0.02648    0.097   100.0    0.072     100
25   K02339  0.564 5.04e-04   0.01266    0.001    50.0    0.000      25
55   K07738  0.565 9.55e-03   0.07465    0.033   100.0    0.021     100
38   K03625  0.567 3.47e-03   0.03487    0.056   100.0    0.043     100
61   K09780  0.579 1.70e-03   0.02130    0.001    58.3    0.000      20
43   K03815  0.580 2.31e-03   0.02644    0.002    50.0    0.001      40
2    K00054  0.581 8.68e-04   0.01496    0.001    58.3    0.000      55
17   K02028  0.584 5.67e-03   0.04924    0.055   100.0    0.045     100
40   K03724  0.585 9.41e-03   0.07376    0.001   100.0    0.000     100
19   K02030  0.586 7.53e-03   0.06196    0.055   100.0    0.044     100
26   K02433  0.619 6.90e-03   0.05766    0.024   100.0    0.019     100
6    K00626  0.625 8.28e-03   0.06672    0.038   100.0    0.025     100
52   K07040  0.626 2.02e-03   0.02387    0.028   100.0    0.019     100
42   K03785  0.643 6.85e-03   0.05736    0.021   100.0    0.012     100
16   K01848  0.655 3.39e-03   0.03425    0.001    75.0    0.000      60
24   K02283  0.664 1.00e-02   0.07763    0.024   100.0    0.014     100
41   K03746  0.667 9.15e-03   0.07234    0.004    75.0    0.001      50
27   K02471  0.675 8.80e-04   0.01512    0.002    91.7    0.000      80
68   K15582  0.678 5.08e-03   0.04565    0.033   100.0    0.022     100
21   K02062  0.679 1.94e-03   0.02308    0.002    83.3    0.000      75
45   K05589  0.690 3.16e-03   0.03252    0.002    50.0    0.000      30
5    K00375  0.696 7.61e-03   0.06236    0.015   100.0    0.010     100
63   K11605  0.701 7.24e-03   0.06008    0.002    91.7    0.001      80
3    K00124  0.702 1.27e-02   0.09428    0.003   100.0    0.001      95
8    K00878  0.710 1.68e-03   0.02130    0.026   100.0    0.017     100
49   K06446  0.710 1.37e-03   0.01899    0.001   100.0    0.001      95
36   K03500  0.717 1.11e-03   0.01682    0.018   100.0    0.011     100
67   K15256  0.735 9.36e-03   0.07366    0.003    66.7    0.001      75
18   K02029  0.738 1.41e-03   0.01933    0.061   100.0    0.042     100
57   K08310  0.742 3.03e-03   0.03155    0.003    66.7    0.001      60
1    K00020  0.743 3.15e-03   0.03244    0.003   100.0    0.000      95
46   K05594  0.748 5.45e-03   0.04795    0.002    66.7    0.001      45
15   K01524  0.766 1.36e-02   0.09929    0.020   100.0    0.014     100
20   K02035  0.767 1.66e-03   0.02120    0.021   100.0    0.012     100
58   K08316  0.770 6.37e-03   0.05399    0.011   100.0    0.006     100
29   K02573  0.772 1.04e-02   0.08011    0.006   100.0    0.003     100
11   K00997  0.780 8.72e-03   0.06945    0.014   100.0    0.009     100
47   K05832  0.781 1.01e-02   0.07811    0.014   100.0    0.009     100
64   K11606  0.793 6.40e-04   0.01343    0.002    83.3    0.000      75
14   K01426  0.798 1.02e-02   0.07845    0.002   100.0    0.001     100
56   K08151  0.798 7.68e-05   0.00679    0.001    66.7    0.001      45
71   K18476  0.801 4.51e-05   0.00608    0.001    75.0    0.001      35
65   K13292  0.806 9.32e-04   0.01566    0.019   100.0    0.011     100
33   K03306  0.808 6.29e-03   0.05340    0.004   100.0    0.002     100
30   K03060  0.809 3.60e-03   0.03569    0.021   100.0    0.013     100
62   K09801  0.809 5.81e-06   0.00436    0.001    58.3    0.000      25
12   K01040  0.827 2.76e-03   0.02954    0.003   100.0    0.002     100
39   K03646  0.834 4.45e-03   0.04180    0.002   100.0    0.001      95
28   K02552  0.835 1.20e-02   0.09023    0.005   100.0    0.002     100
48   K06182  0.837 5.71e-03   0.04941    0.013   100.0    0.007     100
72   K18672  0.845 1.32e-02   0.09710    0.010   100.0    0.005      95
37   K03610  0.860 5.17e-03   0.04619    0.009   100.0    0.004     100
23   K02203  0.886 2.99e-03   0.03128    0.008   100.0    0.004     100
34   K03413  0.890 2.06e-03   0.02418    0.020   100.0    0.010     100
22   K02193  0.902 2.54e-03   0.02772    0.004   100.0    0.002      95
59   K08978  0.915 4.98e-03   0.04501    0.014   100.0    0.007      90
74   K19294  0.919 1.23e-03   0.01772    0.002    91.7    0.000      90
31   K03087  0.954 1.12e-02   0.08489    0.003    58.3    0.001      65
4    K00209  0.985 3.65e-03   0.03613    0.002    91.7    0.001      75
50   K06864  1.028 8.39e-03   0.06723    0.008   100.0    0.003     100
35   K03458  1.031 4.35e-03   0.04120    0.008   100.0    0.004     100
10   K00968  1.033 1.03e-02   0.07918    0.004    75.0    0.002      55
9    K00955  1.099 2.39e-03   0.02663    0.004    75.0    0.001      45
69   K17733  1.327 7.77e-03   0.06342    0.007    66.7    0.002      60

12.5.9 T2 vs T3 (in women with T1D)

  Function  LogFC   P.Val adj.P.Val T2:mean% T2Prev% T3:mean% T3Prev%
3   K01819 -0.613 0.00157     0.572    0.000      40    0.001    56.2
4   K17733  0.519 0.23414     1.000    0.002      60    0.001    50.0
1   K00955  0.568 0.06656     1.000    0.001      45    0.000    50.0
2   K00968  0.587 0.09661     1.000    0.002      55    0.001    56.2

12.5.10 T1 vs T3 (in women with T1D)

    Function  LogFC    P.Val adj.P.Val T1:mean% T1Prev% T3:mean% T3Prev%
19    K00936 -1.099 1.01e-02   0.07302    0.004    91.7    0.007    93.8
186   K18929 -1.007 1.49e-04   0.00982    0.015   100.0    0.025   100.0
131   K07803 -0.895 1.48e-04   0.00982    0.001    16.7    0.002    62.5
128   K07484 -0.827 7.60e-03   0.06041    0.017   100.0    0.024   100.0
27    K01133 -0.824 3.87e-03   0.03764    0.010   100.0    0.017   100.0
185   K18928 -0.786 2.86e-03   0.03052    0.014   100.0    0.023   100.0
106   K05714 -0.775 9.57e-04   0.01750    0.001    33.3    0.002    75.0
75    K02554 -0.751 5.81e-04   0.01560    0.001    41.7    0.002    56.2
134   K08161 -0.728 8.16e-04   0.01659    0.000    66.7    0.001    75.0
156   K11201 -0.720 1.28e-02   0.08536    0.000    66.7    0.003    68.8
161   K12137 -0.699 2.78e-05   0.00625    0.000    25.0    0.001    68.8
99    K04073 -0.688 9.49e-04   0.01750    0.001    41.7    0.002    62.5
9     K00336 -0.677 1.16e-02   0.07984    0.012   100.0    0.021   100.0
153   K10709 -0.648 1.25e-02   0.08437    0.000    50.0    0.002    68.8
115   K06908 -0.634 8.11e-03   0.06328    0.001    16.7    0.001    62.5
144   K09470 -0.611 3.04e-04   0.01352    0.000    41.7    0.001    62.5
16    K00782 -0.609 6.29e-03   0.05277    0.032   100.0    0.048   100.0
10    K00347 -0.565 8.29e-03   0.06373    0.035   100.0    0.055   100.0
135   K08162 -0.563 2.81e-03   0.03029    0.001    50.0    0.001    62.5
30    K01271 -0.559 1.55e-02   0.09757    0.017   100.0    0.023   100.0
42    K01791 -0.551 1.10e-03   0.01856    0.045   100.0    0.068   100.0
139   K08318 -0.550 4.85e-03   0.04391    0.000    16.7    0.001    50.0
4     K00175 -0.543 4.56e-03   0.04215    0.072   100.0    0.111   100.0
61    K02121 -0.539 1.60e-02   0.09954    0.022   100.0    0.032   100.0
145   K09472 -0.510 2.76e-03   0.02993    0.000    25.0    0.001    62.5
140   K08483  0.500 5.01e-03   0.04501    0.035   100.0    0.029   100.0
105   K05685  0.506 2.35e-04   0.01173    0.000    75.0    0.000    37.5
155   K10979  0.508 3.35e-03   0.03406    0.000    66.7    0.000    25.0
174   K15461  0.516 2.81e-04   0.01293    0.001    83.3    0.000    56.2
71    K02455  0.518 1.22e-02   0.08295    0.003    58.3    0.001    50.0
117   K06958  0.529 1.51e-02   0.09579    0.016   100.0    0.013   100.0
7     K00248  0.531 4.13e-03   0.03911    0.013   100.0    0.010   100.0
122   K07124  0.537 8.23e-03   0.06368    0.023   100.0    0.018   100.0
20    K00937  0.538 1.26e-02   0.08446    0.017   100.0    0.015   100.0
66    K02339  0.539 9.51e-04   0.01750    0.001    50.0    0.000    12.5
173   K14475  0.541 1.42e-02   0.09149    0.000    58.3    0.000    31.2
88    K03574  0.541 5.02e-03   0.04501    0.053   100.0    0.040   100.0
170   K14170  0.550 1.06e-02   0.07520    0.022   100.0    0.018   100.0
107   K05874  0.550 3.90e-03   0.03772    0.001    58.3    0.000    31.2
11    K00368  0.552 5.42e-04   0.01529    0.001    58.3    0.000    31.2
166   K13634  0.553 3.64e-04   0.01365    0.001    50.0    0.000    37.5
102   K04759  0.570 5.55e-03   0.04843    0.035   100.0    0.029   100.0
87    K03561  0.570 1.26e-02   0.08466    0.089   100.0    0.069   100.0
36    K01515  0.570 1.61e-02   0.09954    0.025   100.0    0.020   100.0
119   K07095  0.571 2.38e-03   0.02747    0.074   100.0    0.056   100.0
141   K08591  0.571 8.27e-03   0.06368    0.040   100.0    0.030   100.0
48    K01950  0.572 3.92e-03   0.03793    0.111   100.0    0.080   100.0
95    K03724  0.573 1.21e-02   0.08237    0.001   100.0    0.000    93.8
116   K06925  0.578 6.76e-03   0.05551    0.066   100.0    0.046   100.0
51    K02027  0.580 1.21e-02   0.08237    0.038   100.0    0.029   100.0
91    K03601  0.586 7.13e-04   0.01595    0.025   100.0    0.017   100.0
162   K12982  0.587 7.19e-04   0.01595    0.001    50.0    0.000    37.5
40    K01693  0.592 8.21e-03   0.06368    0.031   100.0    0.027   100.0
45    K01848  0.594 8.38e-03   0.06417    0.001    75.0    0.000    68.8
157   K11211  0.597 2.21e-04   0.01144    0.001    58.3    0.000    25.0
52    K02028  0.598 5.19e-03   0.04620    0.055   100.0    0.045   100.0
18    K00878  0.605 7.67e-03   0.06068    0.026   100.0    0.019   100.0
93    K03656  0.619 5.19e-03   0.04620    0.001    91.7    0.000    62.5
12    K00375  0.638 1.52e-02   0.09613    0.015   100.0    0.011   100.0
101   K04096  0.644 1.29e-03   0.02001    0.038   100.0    0.027   100.0
137   K08310  0.645 1.05e-02   0.07429    0.003    66.7    0.001    68.8
133   K08151  0.648 1.31e-03   0.02017    0.001    66.7    0.001    37.5
163   K13243  0.649 1.73e-05   0.00473    0.002    50.0    0.000    43.8
21    K00943  0.650 9.50e-03   0.07046    0.032   100.0    0.023   100.0
1     K00020  0.660 9.38e-03   0.07004    0.003   100.0    0.001    81.2
97    K03923  0.660 9.29e-03   0.06975    0.002    75.0    0.001    68.8
123   K07234  0.662 2.33e-05   0.00555    0.001    66.7    0.000    37.5
183   K18893  0.662 3.56e-05   0.00668    0.001    58.3    0.000    31.2
108   K06042  0.664 1.14e-02   0.07929    0.010   100.0    0.007   100.0
127   K07478  0.672 3.41e-04   0.01358    0.097   100.0    0.067   100.0
67    K02341  0.676 2.98e-04   0.01336    0.052   100.0    0.032   100.0
81    K03216  0.679 1.56e-03   0.02216    0.032   100.0    0.024   100.0
132   K08094  0.680 8.05e-03   0.06291    0.002    58.3    0.000    50.0
118   K07040  0.681 9.50e-04   0.01750    0.028   100.0    0.019   100.0
54    K02030  0.682 2.29e-03   0.02731    0.055   100.0    0.043   100.0
69    K02434  0.685 3.12e-03   0.03254    0.025   100.0    0.020   100.0
70    K02435  0.691 6.76e-03   0.05551    0.020   100.0    0.016   100.0
113   K06446  0.694 1.98e-03   0.02551    0.001   100.0    0.001    93.8
169   K14155  0.697 2.33e-04   0.01173    0.041   100.0    0.027   100.0
187   K19416  0.707 9.34e-05   0.00882    0.001    58.3    0.000    12.5
147   K09780  0.708 1.80e-04   0.01049    0.001    58.3    0.000    12.5
148   K09801  0.715 5.80e-05   0.00722    0.001    58.3    0.000    31.2
176   K15539  0.722 1.35e-02   0.08859    0.003    83.3    0.001    81.2
41    K01749  0.726 5.59e-03   0.04852    0.012   100.0    0.008   100.0
151   K10536  0.728 7.69e-03   0.06072    0.014   100.0    0.010   100.0
96    K03785  0.739 2.25e-03   0.02719    0.021   100.0    0.012   100.0
62    K02193  0.743 1.32e-02   0.08658    0.004   100.0    0.002   100.0
112   K06206  0.748 1.28e-02   0.08509    0.009   100.0    0.005   100.0
73    K02492  0.749 1.53e-02   0.09685    0.010   100.0    0.005   100.0
164   K13292  0.753 2.14e-03   0.02619    0.019   100.0    0.012   100.0
100   K04083  0.753 4.60e-03   0.04232    0.019   100.0    0.012   100.0
171   K14260  0.764 6.70e-03   0.05539    0.010   100.0    0.006   100.0
39    K01626  0.765 5.62e-03   0.04855    0.027   100.0    0.019   100.0
138   K08316  0.767 7.18e-03   0.05770    0.011   100.0    0.006   100.0
26    K01090  0.771 4.47e-03   0.04148    0.010   100.0    0.006   100.0
68    K02433  0.772 9.93e-04   0.01783    0.024   100.0    0.017   100.0
92    K03625  0.772 1.13e-04   0.00952    0.056   100.0    0.039   100.0
78    K03060  0.772 5.86e-03   0.04999    0.021   100.0    0.013   100.0
76    K02654  0.772 6.11e-03   0.05169    0.015   100.0    0.009   100.0
175   K15531  0.773 1.62e-02   0.09978    0.009   100.0    0.005   100.0
126   K07461  0.778 1.02e-02   0.07323    0.026   100.0    0.018    93.8
65    K02334  0.783 1.41e-02   0.09116    0.015   100.0    0.008   100.0
63    K02203  0.785 8.88e-03   0.06728    0.008   100.0    0.005   100.0
120   K07098  0.788 9.43e-04   0.01750    0.044   100.0    0.025   100.0
33    K01494  0.791 1.13e-02   0.07898    0.009   100.0    0.004   100.0
160   K11928  0.796 2.90e-03   0.03083    0.018   100.0    0.013   100.0
85    K03413  0.812 5.24e-03   0.04631    0.020   100.0    0.010   100.0
14    K00641  0.813 8.67e-03   0.06619    0.028   100.0    0.019   100.0
37    K01524  0.813 9.79e-03   0.07170    0.020   100.0    0.015   100.0
53    K02029  0.814 5.38e-04   0.01529    0.061   100.0    0.041   100.0
159   K11606  0.816 5.23e-04   0.01529    0.002    83.3    0.000    68.8
55    K02035  0.829 8.28e-04   0.01659    0.021   100.0    0.012   100.0
64    K02283  0.831 1.62e-03   0.02255    0.024   100.0    0.014   100.0
83    K03273  0.831 1.48e-02   0.09446    0.012   100.0    0.005   100.0
130   K07738  0.832 2.18e-04   0.01144    0.033   100.0    0.020   100.0
177   K17677  0.833 2.22e-03   0.02691    0.008   100.0    0.004   100.0
32    K01436  0.838 1.63e-02   0.09995    0.002    75.0    0.000    81.2
6     K00241  0.847 1.02e-02   0.07323    0.040   100.0    0.025   100.0
80    K03179  0.855 1.48e-02   0.09430    0.015   100.0    0.008   100.0
84    K03306  0.865 3.94e-03   0.03800    0.004   100.0    0.002   100.0
44    K01845  0.866 7.08e-03   0.05714    0.013   100.0    0.011   100.0
124   K07263  0.867 9.33e-03   0.06995    0.013   100.0    0.005   100.0
79    K03074  0.884 1.45e-03   0.02150    0.002    75.0    0.000    50.0
104   K05589  0.898 1.79e-04   0.01049    0.002    50.0    0.000    25.0
158   K11605  0.904 7.19e-04   0.01595    0.002    91.7    0.000    62.5
2     K00104  0.908 1.10e-02   0.07753    0.011   100.0    0.008   100.0
182   K18476  0.910 6.27e-06   0.00356    0.001    75.0    0.001    25.0
150   K09974  0.916 3.57e-03   0.03565    0.011   100.0    0.005   100.0
86    K03500  0.921 4.67e-05   0.00704    0.018   100.0    0.010   100.0
5     K00209  0.923 6.87e-03   0.05595    0.002    91.7    0.000    56.2
50    K02012  0.925 7.63e-03   0.06056    0.005    66.7    0.000    68.8
167   K13788  0.927 6.28e-04   0.01586    0.002    91.7    0.000    68.8
72    K02471  0.930 9.83e-06   0.00356    0.002    91.7    0.000    56.2
24    K00989  0.936 8.77e-03   0.06672    0.013   100.0    0.006   100.0
58    K02062  0.941 3.19e-05   0.00668    0.002    83.3    0.000    43.8
59    K02073  0.950 2.35e-03   0.02737    0.017   100.0    0.008   100.0
25    K00997  0.956 1.62e-03   0.02255    0.014   100.0    0.008   100.0
184   K18926  0.962 9.22e-04   0.01750    0.000    66.7    0.000    68.8
77    K02777  0.963 1.15e-02   0.07953    0.004   100.0    0.003    93.8
35    K01512  0.964 2.28e-03   0.02731    0.013   100.0    0.007   100.0
94    K03684  0.965 8.20e-03   0.06368    0.010   100.0    0.004   100.0
165   K13497  0.966 1.54e-02   0.09697    0.008   100.0    0.009   100.0
29    K01207  0.975 5.20e-03   0.04622    0.019   100.0    0.008   100.0
15    K00690  0.989 1.18e-03   0.01928    0.011   100.0    0.006   100.0
74    K02549  0.999 1.38e-02   0.09023    0.007   100.0    0.003   100.0
129   K07726  1.003 3.70e-03   0.03654    0.011   100.0    0.005   100.0
34    K01496  1.004 1.25e-02   0.08437    0.013   100.0    0.016   100.0
178   K17686  1.004 1.89e-03   0.02475    0.008   100.0    0.004   100.0
47    K01922  1.009 1.58e-02   0.09884    0.005    83.3    0.002    87.5
109   K06077  1.010 1.61e-02   0.09954    0.008    91.7    0.002    93.8
82    K03272  1.011 1.59e-02   0.09910    0.008   100.0    0.003   100.0
46    K01894  1.018 1.26e-02   0.08446    0.006   100.0    0.002    93.8
57    K02050  1.020 1.44e-03   0.02147    0.020   100.0    0.016   100.0
154   K10806  1.041 1.63e-02   0.09995    0.005    83.3    0.001    81.2
3     K00164  1.103 1.45e-02   0.09300    0.005    91.7    0.002    93.8
111   K06195  1.106 1.04e-02   0.07393    0.007    91.7    0.002    93.8
28    K01198  1.107 1.53e-03   0.02193    0.015   100.0    0.007   100.0
172   K14445  1.119 1.55e-02   0.09751    0.011    91.7    0.004   100.0
114   K06864  1.131 4.28e-03   0.04010    0.008   100.0    0.003   100.0
43    K01792  1.136 6.57e-03   0.05465    0.011   100.0    0.003   100.0
98    K03980  1.149 2.84e-03   0.03042    0.008   100.0    0.002   100.0
31    K01304  1.152 6.57e-03   0.05465    0.002    58.3    0.000    62.5
149   K09928  1.162 8.84e-03   0.06708    0.005    75.0    0.001    68.8
143   K09131  1.188 4.84e-03   0.04391    0.008    91.7    0.003    93.8
181   K18095  1.210 1.36e-02   0.08859    0.006    83.3    0.002    93.8
8     K00254  1.211 5.63e-03   0.04857    0.008   100.0    0.002   100.0
17    K00801  1.224 7.23e-03   0.05805    0.004    83.3    0.001    87.5
13    K00380  1.242 1.19e-02   0.08164    0.009   100.0    0.006   100.0
152   K10679  1.244 7.02e-03   0.05680    0.008   100.0    0.003    93.8
142   K08680  1.266 3.15e-03   0.03279    0.008   100.0    0.002   100.0
56    K02049  1.271 2.21e-04   0.01144    0.017   100.0    0.006   100.0
168   K13821  1.278 5.92e-03   0.05040    0.006    83.3    0.002   100.0
49    K02007  1.319 2.73e-03   0.02977    0.010    91.7    0.005    93.8
180   K18094  1.326 3.71e-03   0.03659    0.006    83.3    0.002    87.5
110   K06181  1.338 2.50e-03   0.02806    0.008   100.0    0.002   100.0
60    K02077  1.354 8.90e-04   0.01736    0.007   100.0    0.002   100.0
146   K09769  1.364 6.94e-03   0.05636    0.008   100.0    0.003    93.8
89    K03578  1.367 2.95e-03   0.03119    0.008   100.0    0.004   100.0
136   K08282  1.388 3.63e-03   0.03602    0.006    83.3    0.002    93.8
125   K07318  1.450 1.98e-03   0.02551    0.005    91.7    0.001    62.5
103   K05541  1.455 1.05e-03   0.01817    0.009   100.0    0.002   100.0
90    K03579  1.480 7.27e-04   0.01600    0.004    83.3    0.001    87.5
38    K01598  1.587 8.78e-04   0.01728    0.006    75.0    0.001    62.5
121   K07102  1.610 3.27e-04   0.01358    0.007    83.3    0.001    93.8
23    K00968  1.620 1.15e-04   0.00954    0.004    75.0    0.001    56.2
22    K00955  1.667 9.66e-06   0.00356    0.004    75.0    0.000    50.0
179   K17733  1.846 3.59e-04   0.01358    0.007    66.7    0.001    50.0

12.5.11 T1 vs T2 (in women without T1D)

  Function LogFC    P.Val adj.P.Val T1:mean% T1Prev% T2:mean% T2Prev%
2   K01668 0.680 3.95e-06  0.004329    0.001    81.8    0.000      50
6   K07234 0.786 1.83e-06  0.003338    0.001    90.9    0.001      55
4   K05952 0.860 1.76e-06  0.003338    0.001    63.6    0.000      30
1   K01166 0.883 3.13e-06  0.004291    0.001    81.8    0.000      45
3   K01674 0.892 3.81e-05  0.034838    0.001    90.9    0.001      45
5   K06212 0.941 6.01e-09  0.000033    0.001    90.9    0.000      45

12.5.12 T2 vs T3 (in women without T1D)

[1] "No DA taxa found"

12.5.13 T1 vs T3 (in women without T1D)

   Function  LogFC    P.Val adj.P.Val T1:mean% T1Prev% T3:mean% T3Prev%
16   K02822 -1.537 3.19e-04  4.72e-02    0.002    81.8    0.006   100.0
19   K03293 -1.477 3.59e-04  4.92e-02    0.007   100.0    0.014   100.0
17   K02851 -1.381 3.42e-04  4.81e-02    0.005    90.9    0.008   100.0
11   K01807 -1.311 9.93e-04  9.89e-02    0.007   100.0    0.013   100.0
46   K16925 -1.301 4.34e-04  5.80e-02    0.002    72.7    0.005    88.2
1    K00171 -1.277 4.94e-06  2.46e-03    0.001    81.8    0.005    94.1
6    K01354 -1.261 2.24e-04  3.83e-02    0.001    81.8    0.004    88.2
32   K07467 -1.240 2.45e-05  6.40e-03    0.001    90.9    0.005    94.1
24   K05794 -1.216 6.98e-04  8.14e-02    0.002    81.8    0.005    88.2
21   K03762 -1.189 2.45e-04  4.06e-02    0.001   100.0    0.004   100.0
15   K02588 -1.092 8.62e-04  9.26e-02    0.001   100.0    0.005    94.1
4    K00997 -1.085 5.69e-04  7.26e-02    0.014   100.0    0.023   100.0
8    K01626 -0.957 9.37e-04  9.77e-02    0.018   100.0    0.031   100.0
31   K07454 -0.932 1.22e-05  4.08e-03    0.000    36.4    0.001    70.6
51   K19509 -0.861 5.57e-05  1.22e-02    0.000    45.5    0.001    64.7
33   K07654 -0.852 9.91e-04  9.89e-02    0.000    54.5    0.002    82.4
28   K06605 -0.829 6.05e-04  7.53e-02    0.000    63.6    0.002    76.5
7    K01560 -0.750 3.80e-05  9.05e-03    0.000    27.3    0.001    64.7
48   K18893  0.534 9.45e-04  9.77e-02    0.000    81.8    0.000    35.3
49   K18991  0.542 1.49e-04  2.81e-02    0.000    81.8    0.000    41.2
3    K00979  0.545 8.10e-04  8.88e-02    0.055   100.0    0.041   100.0
47   K18785  0.619 1.84e-04  3.25e-02    0.090   100.0    0.065   100.0
12   K02339  0.629 2.52e-04  4.06e-02    0.000    72.7    0.000    29.4
50   K19431  0.633 2.64e-05  6.59e-03    0.000    81.8    0.000    23.5
44   K15461  0.635 1.81e-05  4.96e-03    0.000    90.9    0.000    52.9
29   K07084  0.658 1.01e-05  3.69e-03    0.000    81.8    0.000    35.3
37   K10094  0.661 1.02e-04  1.99e-02    0.000    72.7    0.000    23.5
18   K03116  0.671 1.68e-04  3.07e-02    0.105   100.0    0.070   100.0
34   K08990  0.676 7.52e-06  3.17e-03    0.000    81.8    0.000    29.4
23   K05685  0.730 5.28e-07  3.62e-04    0.000    90.9    0.000    29.4
2    K00368  0.757 6.68e-06  3.05e-03    0.001    72.7    0.000    29.4
26   K06194  0.758 7.83e-05  1.65e-02    0.001    81.8    0.000    70.6
20   K03656  0.782 6.84e-04  8.14e-02    0.001    90.9    0.000    64.7
42   K12984  0.790 8.55e-05  1.74e-02    0.001    81.8    0.000    41.2
38   K11211  0.803 2.98e-06  1.63e-03    0.001    90.9    0.000    29.4
43   K13634  0.804 1.37e-06  8.36e-04    0.000    72.7    0.000    17.6
41   K12982  0.804 1.27e-05  4.08e-03    0.001    81.8    0.000    23.5
45   K15984  0.848 3.00e-04  4.57e-02    0.001    90.9    0.000    29.4
9    K01668  0.849 3.04e-08  4.17e-05    0.001    81.8    0.000    23.5
40   K12145  0.884 2.95e-04  4.57e-02    0.001    81.8    0.000    29.4
22   K05589  0.894 3.33e-04  4.80e-02    0.001    81.8    0.000    29.4
13   K02344  0.915 1.42e-05  4.33e-03    0.001    81.8    0.000    29.4
39   K11607  0.934 1.85e-07  1.69e-04    0.001    81.8    0.000    29.4
14   K02471  0.946 1.80e-05  4.96e-03    0.001    90.9    0.000    58.8
10   K01674  0.975 9.04e-06  3.54e-03    0.001    90.9    0.000    29.4
5    K01166  0.999 2.17e-07  1.70e-04    0.001    81.8    0.000    29.4
35   K09801  0.999 1.58e-07  1.69e-04    0.001    81.8    0.000    23.5
36   K09824  1.017 4.02e-05  9.17e-03    0.001    81.8    0.000    52.9
25   K05952  1.022 2.84e-08  4.17e-05    0.001    63.6    0.000    11.8
27   K06212  1.029 4.13e-10  2.26e-06    0.001    90.9    0.000    35.3
30   K07234  1.031 1.93e-09  5.27e-06    0.001    90.9    0.000    35.3
[1] 20

13 Functional analysis (MetaCyc reactions)

13.1 Bar plots taxonomy

13.2 Functional Alpha diversity (Days)

13.3 Functional Alpha diversity (Trimesters)


Call:
geeglm(formula = Observed ~ t1dfactor * Tri + age_c + nullip + 
    bmi_c + HLA + SeqRun, data = DivCal_R_df, id = motherid, 
    corstr = "exchangeable")

 Coefficients:
                   Estimate Std.err   Wald Pr(>|W|)    
(Intercept)         1883.99   66.29 807.78   <2e-16 ***
t1dfactorT1D         138.79   86.88   2.55    0.110    
TriT2                 71.54   52.33   1.87    0.172    
TriT3                 94.49   62.93   2.25    0.133    
age_c                  3.76    5.27   0.51    0.476    
nullipYes            -97.91   39.52   6.14    0.013 *  
bmi_c                  1.47    4.55   0.10    0.747    
HLADRXX               28.64   53.34   0.29    0.591    
HLAGroup3o4           44.08   49.75   0.78    0.376    
SeqRun3               38.76   48.95   0.63    0.428    
SeqRun4               82.61   50.33   2.69    0.101    
SeqRun6              -11.79   58.00   0.04    0.839    
t1dfactorT1D:TriT2   -94.46   97.11   0.95    0.331    
t1dfactorT1D:TriT3  -116.83  101.27   1.33    0.249    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Estimated Scale Parameters:
            Estimate Std.err
(Intercept)    29167    5010

Correlation: Structure = exchangeable  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha    0.115   0.178
Number of clusters:   83   Maximum cluster size: 3 

13.4 Beta diversity analysis

13.4.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                     Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun                3     0.096  0.0318    1.85 0.051  0.001 ***
Days                  1     0.018  0.0181    1.05 0.010  0.110    
T1D_Time_Interaction  1     0.094  0.0939    5.45 0.050  0.049 *  
Age                   1     0.058  0.0583    3.38 0.031  0.991    
Parity                1     0.038  0.0380    2.20 0.020  0.184    
BMI                   1     0.029  0.0290    1.68 0.015  0.971    
HLA                   2     0.074  0.0370    2.15 0.039  0.593    
T1Dstatus             1     0.022  0.0224    1.30 0.012  0.901    
Residuals            84     1.448  0.0172         0.771  0.612    
Total                95     1.877                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.049

13.4.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3     0.040  0.0134   0.583 0.084   0.96
Nulliparous     1     0.023  0.0227   0.984 0.048   0.47
Age_LMP         1     0.023  0.0227   0.985 0.048   0.45
BMI_conception  1     0.016  0.0156   0.677 0.033   0.75
HLA.6DRML       2     0.040  0.0202   0.875 0.084   0.64
T1Dstatus       1     0.036  0.0363   1.572 0.076   0.11
Residuals      13     0.300  0.0231         0.628       
Total          22     0.478                 1.000       
[1] 0.113

Beta diversity Plot

13.4.3 T1D status in trimester 2


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3     0.067  0.0223   1.184 0.112   0.24
Nulliparous     1     0.021  0.0212   1.125 0.035   0.33
Age_LMP         1     0.026  0.0261   1.383 0.044   0.18
BMI_conception  1     0.010  0.0103   0.548 0.017   0.87
HLA.6DRML       2     0.035  0.0175   0.927 0.058   0.54
T1Dstatus       1     0.023  0.0233   1.240 0.039   0.25
Residuals      22     0.414  0.0188         0.694       
Total          31     0.597                 1.000       
[1] 0.247

Beta diversity Plot

13.4.4 T1D status in trimester 3


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
SeqRun          3     0.041  0.0136   0.643 0.062  0.934   
Nulliparous     1     0.016  0.0162   0.769 0.025  0.660   
Age_LMP         1     0.022  0.0222   1.052 0.034  0.390   
BMI_conception  1     0.022  0.0220   1.039 0.033  0.407   
HLA.6DRML       2     0.032  0.0162   0.768 0.049  0.756   
T1Dstatus       1     0.063  0.0626   2.964 0.095  0.004 **
Residuals      22     0.465  0.0211         0.703          
Total          31     0.661                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.004

Beta diversity Plot

13.4.5 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.060  0.0301    1.97 0.067   0.72
seqRun     3     0.096  0.0320    2.09 0.107   0.73
Age        1     0.025  0.0252    1.65 0.028   0.93
Parity     1     0.081  0.0806    5.28 0.090   0.10
BMI        1     0.048  0.0479    3.14 0.053   0.40
Tri        2     0.023  0.0113    0.74 0.025   0.40
Residuals 37     0.565  0.0153         0.630   0.80
Total     47     0.897                 1.000       

Beta diversity Plot

13.4.6 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.085  0.0425    3.03 0.097  0.390  
seqRun     3     0.091  0.0305    2.17 0.104  0.848  
Age        1     0.101  0.1009    7.19 0.115  0.099 .
Parity     1     0.024  0.0242    1.73 0.027  0.955  
BMI        1     0.040  0.0396    2.82 0.045  0.042 *
Tri        2     0.020  0.0101    0.72 0.023  0.492  
Residuals 37     0.519  0.0140         0.590  0.324  
Total     47     0.880                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

13.5 Differential abundance analysis

Controlling for multiple measurements, sequencing run, conception age, BMI, parity and HLA type

       nonT1D_vs_T1D   T1   T2   T3 T1_vs_T2 T2_vs_T3 T1_vs_T3 T1DT1vsT2 T1DT2vsT3
Down               0   17    0    0        0        0        1         0         0
NotSig          3014 2996 3014 3003     3014     3014     3009      3014      3014
Up                 0    1    0   11        0        0        4         0         0
       T1DT1vsT3 noT1DT1vsT2 noT1DT2vsT3 noT1DT1vsT3
Down           1           0           0           1
NotSig      2997        3014        3014        3009
Up            16           0           0           4

Results for contrasts with significant differentially abundant strains shown below

13.5.1 Across all trimesters (T1D vs non-T1D)

[1] "No DA taxa found"

13.5.2 Only Trimester 1 (nonT1D vs T1D)

        Function  LogFC    P.Val adj.P.Val nonT1D:mean% Prev% T1D:mean% T1D:Prev%
2  DHBAMPLIG-RXN -2.051 1.04e-04    0.0224        0.001 100.0     0.004     100.0
6      RXN-14814 -2.051 1.04e-04    0.0224        0.001 100.0     0.004     100.0
1  3.4.21.87-RXN -1.426 1.77e-05    0.0213        0.000  50.0     0.000      37.5
7       RXN0-305 -1.420 8.08e-05    0.0213        0.000  56.2     0.001      75.0
5      RXN-12444 -1.190 7.48e-04    0.0835        0.000  68.8     0.001      56.2
3        R15-RXN -1.140 4.68e-04    0.0613        0.000  68.8     0.001      68.8
4      RXN-12353 -0.966 1.84e-04    0.0309        0.000  37.5     0.000      62.5
8       RXN0-984 -0.966 1.84e-04    0.0309        0.000  37.5     0.000      62.5
9       RXN0-985 -0.966 1.84e-04    0.0309        0.000  37.5     0.000      62.5
10      RXN0-986 -0.966 1.84e-04    0.0309        0.000  37.5     0.000      62.5

13.5.3 Only Trimester 2 (nonT1D vs T1D)

[1] "No DA taxa found"

13.5.4 Only Trimester 3 (nonT1D vs T1D)

                               Function  LogFC    P.Val adj.P.Val nonT1D:mean% Prev%
27                            RXN-14469 -1.149 2.95e-04   0.05930        0.000  43.8
11      CYSTATHIONINE-BETA-SYNTHASE-RXN  0.938 4.78e-04   0.08094        0.001  56.2
6                 ADENINE-DEAMINASE-RXN  0.958 1.03e-03   0.09978        0.045 100.0
21                            RXN-11860  1.009 5.16e-04   0.08094        0.059 100.0
22                            RXN-11865  1.009 5.16e-04   0.08094        0.059 100.0
14                GLUC1PADENYLTRANS-RXN  1.032 9.10e-04   0.09794        0.147 100.0
15                     GLUTAMATESYN-RXN  1.093 9.60e-04   0.09972        0.085 100.0
30                      THIAZOLSYN3-RXN  1.132 6.56e-04   0.08094        0.048 100.0
26                            RXN-14148  1.140 4.28e-05   0.01844        0.002  56.2
13              GALACTURIDYLYLTRANS-RXN  1.159 5.16e-04   0.08094        0.049 100.0
7   BRANCHED-CHAINAMINOTRANSFERILEU-RXN  1.168 7.67e-05   0.02312        0.060 100.0
8    BRANCHED-CHAINAMINOTRANSFERLEU-RXN  1.168 7.67e-05   0.02312        0.060 100.0
9    BRANCHED-CHAINAMINOTRANSFERVAL-RXN  1.168 7.67e-05   0.02312        0.060 100.0
4                           6.3.5.7-RXN  1.191 6.98e-04   0.08094        0.065 100.0
2                         3.4.21.88-RXN  1.200 5.54e-04   0.08094        0.057 100.0
20                            RXN-11322  1.222 2.67e-04   0.05746        0.076 100.0
28                             RXN-2043  1.239 6.85e-04   0.08094        0.033 100.0
3    5-DEHYDRO-2-DEOXYGLUCONOKINASE-RXN  1.259 1.32e-04   0.03621        0.001  68.8
17                   PHOSPHAGLYPSYN-RXN  1.293 2.40e-04   0.05746        0.063 100.0
29                             RXN-8850  1.369 9.98e-04   0.09978        0.034 100.0
5                   ACYLPHOSPHATASE-RXN  1.404 2.59e-04   0.05746        0.015 100.0
12              DIHYDROPYRIMIDINASE-RXN  1.518 6.45e-04   0.08094        0.003  93.8
18                            RXN-11211  1.518 6.45e-04   0.08094        0.003  93.8
19                            RXN-11217  1.518 6.45e-04   0.08094        0.003  93.8
16        MYO-INOSOSE-2-DEHYDRATASE-RXN  1.661 8.06e-04   0.08994        0.005 100.0
10             CYCLOMALTODEXTRINASE-RXN  1.827 4.25e-06   0.00320        0.003  68.8
1                         1.1.1.188-RXN  1.878 3.82e-05   0.01844        0.004  62.5
23                            RXN-12558  1.956 2.03e-06   0.00204        0.005  87.5
24                            RXN-12559  1.956 2.03e-06   0.00204        0.005  87.5
31 TRANS-2-ENOYL-COA-REDUCTASE-NAD+-RXN  1.956 2.03e-06   0.00204        0.005  87.5
25                            RXN-13028  2.348 4.01e-05   0.01844        0.007  87.5
   T1D:mean% T1D:Prev%
27     0.001      68.8
11     0.000      18.8
6      0.031     100.0
21     0.033     100.0
22     0.033     100.0
14     0.087     100.0
15     0.053     100.0
30     0.025     100.0
26     0.000      25.0
13     0.029     100.0
7      0.032     100.0
8      0.032     100.0
9      0.032     100.0
4      0.032     100.0
2      0.032     100.0
20     0.037     100.0
28     0.017     100.0
3      0.000      43.8
17     0.033     100.0
29     0.017     100.0
5      0.008     100.0
12     0.001      87.5
18     0.001      87.5
19     0.001      87.5
16     0.002      87.5
10     0.000      43.8
1      0.000      43.8
23     0.000      56.2
24     0.000      56.2
31     0.000      56.2
25     0.000      81.2

13.5.5 T1 vs T2 (All data)

[1] "No DA taxa found"

13.5.6 T2 vs T3 (All data)

[1] "No DA taxa"

13.5.7 T1 vs T3 (All data)

                          Function  LogFC    P.Val adj.P.Val T1:mean% T1Prev% T2:mean%
1 2-OXOPENT-4-ENOATE-HYDRATASE-RXN -0.537 1.64e-04  8.22e-02    0.000    47.8    0.001
2                     3.1.21.1-RXN -0.934 8.72e-06  5.25e-03    0.001    47.8    0.001
3                    3.4.24.57-RXN  0.701 5.75e-06  4.33e-03    0.001    69.6    0.000
4             6PGLUCONDEHYDROG-RXN  0.784 1.32e-06  1.33e-03    0.001    82.6    0.000
5                        RXN-11328  0.711 8.34e-09  1.26e-05    0.001    73.9    0.000
6                        RXN-16750  0.711 8.34e-09  1.26e-05    0.001    73.9    0.000
  T2Prev% T3:mean% T3Prev%
1    42.5    0.001    63.6
2    57.5    0.001    75.8
3    50.0    0.000    33.3
4    75.0    0.000    39.4
5    50.0    0.000    27.3
6    50.0    0.000    27.3

13.5.8 T1 vs T2 (in women with T1D)

[1] "No DA taxa found"

13.5.9 T2 vs T3 (in women with T1D)

[1] "No DA taxa found"

13.5.10 T1 vs T3 (in women with T1D)

                               Function  LogFC    P.Val adj.P.Val T1:mean% T1Prev%
7                          3.1.21.1-RXN -1.064 2.53e-04    0.0448    0.001    50.0
31     N-ACETYLNEURAMINATE-SYNTHASE-RXN -0.965 2.57e-03    0.0712    0.001    66.7
58                            RXN0-5228 -0.727 4.84e-03    0.0844    0.009   100.0
38                            RXN-11596 -0.700 1.03e-02    0.0948    0.009   100.0
30                       MHPCHYDROL-RXN -0.684 1.20e-03    0.0544    0.000    33.3
41                            RXN-12070 -0.684 1.20e-03    0.0544    0.000    33.3
3      2-OXOPENT-4-ENOATE-HYDRATASE-RXN -0.662 8.68e-04    0.0544    0.001    41.7
49                            RXN-15299 -0.647 4.07e-04    0.0544    0.000    16.7
18                              GKI-RXN -0.543 8.14e-04    0.0544    0.000    33.3
4                          2.1.1.72-RXN  0.508 4.02e-03    0.0787    0.235   100.0
54                             RXN-8668  0.527 1.91e-03    0.0695    0.054   100.0
37                            RXN-11328  0.533 8.35e-04    0.0544    0.001    58.3
51                            RXN-16750  0.533 8.35e-04    0.0544    0.001    58.3
24                  H2PTEROATESYNTH-RXN  0.549 1.21e-03    0.0544    0.038   100.0
55                             RXN0-305  0.551 8.88e-03    0.0948    0.003    75.0
26                       HOMOSERKIN-RXN  0.552 3.04e-03    0.0718    0.040   100.0
5                           2.7.9.3-RXN  0.553 8.36e-03    0.0948    0.022   100.0
13                          AMIDASE-RXN  0.559 7.36e-06    0.0037    0.001    66.7
22          GUANIDINOBUTANAMIDE-NH3-RXN  0.559 7.36e-06    0.0037    0.001    66.7
34                             R311-RXN  0.559 7.36e-06    0.0037    0.001    66.7
47                            RXN-14727  0.559 7.36e-06    0.0037    0.001    66.7
48                            RXN-14728  0.559 7.36e-06    0.0037    0.001    66.7
66                             RXNN-404  0.559 7.36e-06    0.0037    0.001    66.7
39                            RXN-11860  0.562 3.07e-03    0.0718    0.044   100.0
40                            RXN-11865  0.562 3.07e-03    0.0718    0.044   100.0
23    H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN  0.598 6.35e-03    0.0894    0.002    66.7
19                GLUC1PURIDYLTRANS-RXN  0.613 7.75e-03    0.0948    0.027   100.0
44                            RXN-14047  0.625 9.78e-03    0.0948    0.013   100.0
16                           DTMPKI-RXN  0.646 2.32e-03    0.0712    0.041   100.0
29                        MANNPISOM-RXN  0.650 1.98e-03    0.0701    0.051   100.0
67                      THIAZOLSYN3-RXN  0.655 2.57e-03    0.0712    0.037   100.0
17                            ENTDB-RXN  0.671 1.05e-02    0.0956    0.027   100.0
50                            RXN-15889  0.671 1.05e-02    0.0956    0.027   100.0
33                   PORPHOBILSYNTH-RXN  0.696 5.78e-03    0.0872    0.022   100.0
12                  ACYLPHOSPHATASE-RXN  0.705 4.71e-03    0.0843    0.012   100.0
25                   HOLO-ACP-SYNTH-RXN  0.718 5.77e-03    0.0872    0.027   100.0
35                            RXN-10994  0.718 5.77e-03    0.0872    0.027   100.0
52                            RXN-16759  0.718 5.77e-03    0.0872    0.027   100.0
21                    GSAAMINOTRANS-RXN  0.723 6.35e-03    0.0894    0.021   100.0
46                            RXN-14569  0.729 1.81e-03    0.0684    0.026   100.0
9                         3.1.26.12-RXN  0.763 1.35e-03    0.0544    0.001    50.0
59                            RXN0-6478  0.763 1.35e-03    0.0544    0.001    50.0
60                            RXN0-6485  0.763 1.35e-03    0.0544    0.001    50.0
62                            RXN0-6521  0.763 1.35e-03    0.0544    0.001    50.0
63                            RXN0-6522  0.763 1.35e-03    0.0544    0.001    50.0
64                            RXN0-6523  0.763 1.35e-03    0.0544    0.001    50.0
15     DIHYDROOROTATE-DEHYDROGENASE-RXN  0.764 8.78e-03    0.0948    0.025   100.0
61                            RXN0-6491  0.764 8.78e-03    0.0948    0.025   100.0
65                            RXN0-6554  0.764 8.78e-03    0.0948    0.025   100.0
32                OHMETHYLBILANESYN-RXN  0.787 3.81e-04    0.0544    0.019   100.0
53                             RXN-7644  0.803 7.91e-04    0.0544    0.013   100.0
11                         6.1.1.23-RXN  0.808 3.26e-04    0.0544    0.001    66.7
2                           1.3.1.2-RXN  0.808 9.40e-03    0.0948    0.001    75.0
36                            RXN-11209  0.808 9.40e-03    0.0948    0.001    75.0
27         L-IDITOL-2-DEHYDROGENASE-RXN  0.816 5.55e-04    0.0544    0.013   100.0
10                        3.4.21.87-RXN  0.822 3.07e-05    0.0103    0.001    58.3
56                            RXN0-3281  0.837 2.22e-04    0.0440    0.002    66.7
57                            RXN0-4301  0.855 4.32e-03    0.0811    0.013   100.0
14                        DCTP-DEAM-RXN  0.857 5.68e-03    0.0872    0.009   100.0
45                            RXN-14118  0.857 5.68e-03    0.0872    0.009   100.0
42                            RXN-12558  0.864 1.11e-03    0.0544    0.001    83.3
43                            RXN-12559  0.864 1.11e-03    0.0544    0.001    83.3
68 TRANS-2-ENOYL-COA-REDUCTASE-NAD+-RXN  0.864 1.11e-03    0.0544    0.001    83.3
28                      LYSDECARBOX-RXN  0.921 5.18e-03    0.0856    0.002    91.7
1                           1.2.1.2-RXN  0.980 9.42e-03    0.0948    0.005    91.7
20                    GLUTRNAREDUCT-RXN  1.013 6.05e-04    0.0544    0.014   100.0
8                          3.1.21.5-RXN  1.085 1.53e-03    0.0598    0.002   100.0
6                    2OXOGLUTDECARB-RXN  1.166 9.10e-03    0.0948    0.004    91.7
   T3:mean% T3Prev%
7     0.002    87.5
31    0.002    68.8
58    0.014   100.0
38    0.014   100.0
30    0.001    75.0
41    0.001    75.0
3     0.001    56.2
49    0.001    50.0
18    0.001    50.0
4     0.188   100.0
54    0.041   100.0
37    0.000    25.0
51    0.000    25.0
24    0.025   100.0
55    0.001    75.0
26    0.028   100.0
5     0.016   100.0
13    0.000    43.8
22    0.000    43.8
34    0.000    43.8
47    0.000    43.8
48    0.000    43.8
66    0.000    43.8
39    0.033   100.0
40    0.033   100.0
23    0.001    56.2
19    0.018   100.0
44    0.010   100.0
16    0.031   100.0
29    0.036   100.0
67    0.025   100.0
17    0.017   100.0
50    0.017   100.0
33    0.015   100.0
12    0.008   100.0
25    0.017   100.0
35    0.017   100.0
52    0.017   100.0
21    0.016   100.0
46    0.017   100.0
9     0.000    31.2
59    0.000    31.2
60    0.000    31.2
62    0.000    31.2
63    0.000    31.2
64    0.000    31.2
15    0.018   100.0
61    0.018   100.0
65    0.018   100.0
32    0.011   100.0
53    0.008   100.0
11    0.000    31.2
2     0.000    75.0
36    0.000    75.0
27    0.008   100.0
10    0.000    37.5
56    0.001    50.0
57    0.007   100.0
14    0.004   100.0
45    0.004   100.0
42    0.000    56.2
43    0.000    56.2
68    0.000    56.2
28    0.001    93.8
1     0.001    87.5
20    0.007   100.0
8     0.002    68.8
6     0.001   100.0

13.5.11 T1 vs T2 (in women without T1D)

[1] "No DA taxa found"

13.5.12 T2 vs T3 (in women without T1D)

    Function  LogFC    P.Val adj.P.Val mean% Prev%
T2 RXN-14148 -0.663 2.69e-05    0.0811 0.000  30.0
T3 RXN-14148 -0.663 2.69e-05    0.0811 0.002  58.8

13.5.13 T1 vs T3 (in women without T1D)

               Function  LogFC    P.Val adj.P.Val T1:mean% T1Prev% T3:mean% T3Prev%
6 NAG1P-URIDYLTRANS-RXN -1.317 2.20e-04  0.076366    0.002   100.0    0.006   100.0
5              MMUM-RXN -1.152 3.16e-04  0.095382    0.000    90.9    0.003    88.2
4      HISTCYCLOHYD-RXN -1.101 1.01e-04  0.050762    0.021   100.0    0.042   100.0
1         3.4.21.83-RXN -1.095 5.99e-05  0.036124    0.000    72.7    0.002    76.5
7             RXN-11328  0.889 3.17e-07  0.000478    0.000    90.9    0.000    29.4
8             RXN-16750  0.889 3.17e-07  0.000478    0.000    90.9    0.000    29.4
2         3.4.24.57-RXN  1.037 4.58e-06  0.003449    0.001    90.9    0.000    41.2
3  6PGLUCONDEHYDROG-RXN  1.127 1.31e-06  0.001320    0.001    90.9    0.000    41.2
[1] 28